From a7a13ffec4905a850d37396260730884845c8add Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 16 Oct 2025 14:23:38 -0400 Subject: [PATCH 01/65] implementing gtars qc --- ui/package-lock.json | 15 +++++ ui/package.json | 6 +- ui/src/main.tsx | 5 ++ ui/src/pages/bed-analytics.tsx | 112 +++++++++++++++++++++++++++++++++ ui/src/utils.ts | 64 +++++++++++++++++++ 5 files changed, 200 insertions(+), 2 deletions(-) create mode 100644 ui/src/pages/bed-analytics.tsx diff --git a/ui/package-lock.json b/ui/package-lock.json index 8e03fbf4..cd99975a 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -19,7 +19,9 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", + "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", + "pako": "^2.1.0", "react": "^18.2.0", "react-bootstrap": "^2.10.1", "react-chartjs-2": "^5.2.0", @@ -50,6 +52,10 @@ "vite": "^6.3.6" } }, + "../../gtars/gtars-wasm/pkg": { + "name": "gtars-js", + "version": "0.5.0" + }, "node_modules/@aashutoshrathi/word-wrap": { "version": "1.2.6", "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", @@ -2832,6 +2838,10 @@ "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==", "dev": true }, + "node_modules/gtars-js": { + "resolved": "../../gtars/gtars-wasm/pkg", + "link": true + }, "node_modules/hast-util-is-element": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/hast-util-is-element/-/hast-util-is-element-3.0.0.tgz", @@ -4090,6 +4100,11 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/pako": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/pako/-/pako-2.1.0.tgz", + "integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug==" + }, "node_modules/parent-module": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz", diff --git a/ui/package.json b/ui/package.json index 081c74b0..7ccc253f 100644 --- a/ui/package.json +++ b/ui/package.json @@ -23,7 +23,9 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", + "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", + "pako": "^2.1.0", "react": "^18.2.0", "react-bootstrap": "^2.10.1", "react-chartjs-2": "^5.2.0", @@ -35,8 +37,8 @@ "react-markdown": "^9.0.1", "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", - "vega-embed": "^7.0.2", - "three": "^0.177.0" + "three": "^0.177.0", + "vega-embed": "^7.0.2" }, "devDependencies": { "@types/js-yaml": "^4.0.9", diff --git a/ui/src/main.tsx b/ui/src/main.tsx index df411949..929d43c3 100644 --- a/ui/src/main.tsx +++ b/ui/src/main.tsx @@ -9,6 +9,7 @@ import toast, { Toaster } from 'react-hot-toast'; import { Home } from './pages/home.tsx'; import { Metrics } from './pages/metrics.tsx'; import { UMAPGraph } from './pages/visualization.tsx'; +import { BEDAnalytics } from './pages/bed-analytics.tsx'; import { HelmetProvider } from 'react-helmet-async'; // css stuff @@ -79,6 +80,10 @@ const router = createBrowserRouter([ path: '/umap', element: , }, + { + path: '/qc', + element: , + }, ]); // entry point diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx new file mode 100644 index 00000000..c9e661eb --- /dev/null +++ b/ui/src/pages/bed-analytics.tsx @@ -0,0 +1,112 @@ +import { useState, useRef } from 'react'; +import { Layout } from '../components/layout.tsx'; +import { RegionSet } from 'gtars-js'; +import { handleBedFileInput, type BedEntry } from '../utils.ts'; + +export const BEDAnalytics = () => { + const [regionsetRegions, setregionsetRegions] = useState(null); + const [Rs, setRs] = useState(null); + const [loadingRS, setLoadingRS] = useState(false); + const regionsetFileInputRef = useRef(null); + + const initializeRegionSet = (regionsetRegions) => { + if (regionsetRegions) { + console.log('initializing regionset'); + console.log(regionsetRegions); + setLoadingRS(true); + const rs = new RegionSet(regionsetRegions); + setRs(rs); + setLoadingRS(false); + } else { + setLoadingRS(false); + } + }; + + return ( + +
+
+ + { + const input = e.target as HTMLInputElement; + const file = input.files?.[0]; + if (file) { + // @ts-expect-error its fine :) + handleBedFileInput(e, (entries) => { + setregionsetRegions(entries); + }); + } + }} + /> + {regionsetRegions && ( +

+ {regionsetRegions.length} regions in universe +

+ )} +
+ +
+ {Rs &&

RegionSet initialized with {Rs.get_phi} regions

} +
+ +
+ + +
+ +
+
+
+ + RegionSet ready + +
+
+ {Rs && ( +
+

Mean region width: {Rs.mean_region_width}

+

Total number of regions: {Rs.number_of_regions}

+

Total number of nucleotides: {Rs.total_nucleotides}

+
+ )} +
+
+
+ + ); +}; \ No newline at end of file diff --git a/ui/src/utils.ts b/ui/src/utils.ts index 4cc01e5b..9e32655d 100644 --- a/ui/src/utils.ts +++ b/ui/src/utils.ts @@ -1,3 +1,5 @@ +import * as pako from 'pako'; + type ObjectType = 'bed' | 'bedset'; export const makeHttpDownloadLink = (md5: string) => { @@ -135,3 +137,65 @@ export const convertStatusCodeToMessage = (statusCode: number | undefined) => { return 'Unknown Error'; } }; + +// gtars bedfile handler +export type BedEntry = [string, number, number, string]; + +export async function parseBedFile(file: File): Promise { + let text: string; + if (file.name.endsWith('.gz')) { + const arrayBuffer = await file.arrayBuffer(); + const decompressed = pako.ungzip(new Uint8Array(arrayBuffer), { to: 'string' }); + text = decompressed; + } else { + text = await file.text(); + } + const lines = text.split('\n'); + const bedEntries: BedEntry[] = []; + +// export async function parseBedFile(file: File): Promise { +// const text = await file.text(); +// const lines = text.split('\n'); +// const bedEntries: BedEntry[] = []; + + for (const line of lines) { + const trimmedLine = line.trim(); + + // skip! + if (!trimmedLine || trimmedLine.startsWith('#')) { + continue; + } + + const columns = trimmedLine.split('\t'); + + // check for at least 3 columns (chr, start, end) + if (columns.length >= 3) { + const chr = columns[0]; + const start = parseInt(columns[1], 10); + const end = parseInt(columns[2], 10); + const rest = columns.slice(3).join('\t'); // join remaining columns if any + + // Validate that start and end are valid numbers + if (!isNaN(start) && !isNaN(end)) { + bedEntries.push([chr, start, end, rest]); + } + } + } + + return bedEntries; +} + +// helper function to handle file input change event +export function handleBedFileInput( + event: Event, + callback: (entries: BedEntry[]) => void +): void { + const input = event.target as HTMLInputElement; + const file = input.files?.[0]; + + if (file) { + parseBedFile(file) + .then(callback) + .catch((error) => console.error('Error parsing BED file:', error)); + } +} From e5864cd82f7b7f62cd062ee206c1e04d6c9c2e35 Mon Sep 17 00:00:00 2001 From: Nathan LeRoy Date: Thu, 16 Oct 2025 15:42:03 -0400 Subject: [PATCH 02/65] update pkgs and files vite config --- ui/package-lock.json | 4773 +++++++++++++++++++++----------- ui/package.json | 6 +- ui/src/pages/bed-analytics.tsx | 2 +- ui/vite.config.ts | 12 +- 4 files changed, 3230 insertions(+), 1563 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index cd99975a..55c99c46 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -8,6 +8,7 @@ "name": "bedhost-ui-2", "version": "0.0.0", "dependencies": { + "@databio/gtars": "file:../../gtars/gtars-wasm/pkg", "@tanstack/react-query": "^5.28.0", "@tanstack/react-query-devtools": "^5.28.0", "@tanstack/react-table": "^8.15.3", @@ -19,7 +20,6 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", - "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", "pako": "^2.1.0", "react": "^18.2.0", @@ -34,7 +34,9 @@ "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", "three": "^0.177.0", - "vega-embed": "^7.0.2" + "vega-embed": "^7.0.2", + "vite-plugin-top-level-await": "^1.6.0", + "vite-plugin-wasm": "^3.5.0" }, "devDependencies": { "@types/js-yaml": "^4.0.9", @@ -53,51 +55,28 @@ } }, "../../gtars/gtars-wasm/pkg": { - "name": "gtars-js", + "name": "@databio/gtars", "version": "0.5.0" }, - "node_modules/@aashutoshrathi/word-wrap": { - "version": "1.2.6", - "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", - "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==", - "dev": true, - "engines": { - "node": ">=0.10.0" - } - }, - "node_modules/@ampproject/remapping": { - "version": "2.3.0", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", - "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", - "dev": true, - "license": "Apache-2.0", - "dependencies": { - "@jridgewell/gen-mapping": "^0.3.5", - "@jridgewell/trace-mapping": "^0.3.24" - }, - "engines": { - "node": ">=6.0.0" - } - }, "node_modules/@babel/code-frame": { - "version": "7.26.2", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.26.2.tgz", - "integrity": "sha512-RJlIHRueQgwWitWgF8OdFYGZX328Ax5BCemNGlqHfplnRT9ESi8JkFlvaVYbS+UubVY6dpv87Fs2u5M29iNFVQ==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.27.1.tgz", + "integrity": "sha512-cjQ7ZlQ0Mv3b47hABuTevyTuYN4i+loJKGeV9flcCgIK37cCXRh+L1bd3iBHlynerhQ7BhCkn2BPbQUL+rGqFg==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-validator-identifier": "^7.25.9", + "@babel/helper-validator-identifier": "^7.27.1", "js-tokens": "^4.0.0", - "picocolors": "^1.0.0" + "picocolors": "^1.1.1" }, "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/compat-data": { - "version": "7.26.8", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.26.8.tgz", - "integrity": "sha512-oH5UPLMWR3L2wEFLnFJ1TZXqHufiTKAiLfqw5zkhS4dKXLJ10yVztfil/twG8EDTA4F/tvVNw9nOl4ZMslB8rQ==", + "version": "7.28.4", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.4.tgz", + "integrity": "sha512-YsmSKC29MJwf0gF8Rjjrg5LQCmyh+j/nD8/eP7f+BeoQTKYqs9RoWbjGOdy0+1Ekr68RJZMUOPVQaQisnIo4Rw==", "dev": true, "license": "MIT", "engines": { @@ -105,22 +84,22 @@ } }, "node_modules/@babel/core": { - "version": "7.26.10", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.10.tgz", - "integrity": "sha512-vMqyb7XCDMPvJFFOaT9kxtiRh42GwlZEg1/uIgtZshS5a/8OaduUfCi7kynKgc3Tw/6Uo2D+db9qBttghhmxwQ==", - "dev": true, - "license": "MIT", - "dependencies": { - "@ampproject/remapping": "^2.2.0", - "@babel/code-frame": "^7.26.2", - "@babel/generator": "^7.26.10", - "@babel/helper-compilation-targets": "^7.26.5", - "@babel/helper-module-transforms": "^7.26.0", - "@babel/helpers": "^7.26.10", - "@babel/parser": "^7.26.10", - "@babel/template": "^7.26.9", - "@babel/traverse": "^7.26.10", - "@babel/types": "^7.26.10", + "version": "7.28.4", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.4.tgz", + "integrity": "sha512-2BCOP7TN8M+gVDj7/ht3hsaO/B/n5oDbiAyyvnRlNOs+u1o+JWNYTQrmpuNp1/Wq2gcFrI01JAW+paEKDMx/CA==", + "dev": true, + "license": "MIT", + "dependencies": { + "@babel/code-frame": "^7.27.1", + "@babel/generator": "^7.28.3", + "@babel/helper-compilation-targets": "^7.27.2", + "@babel/helper-module-transforms": "^7.28.3", + "@babel/helpers": "^7.28.4", + "@babel/parser": "^7.28.4", + "@babel/template": "^7.27.2", + "@babel/traverse": "^7.28.4", + "@babel/types": "^7.28.4", + "@jridgewell/remapping": "^2.3.5", "convert-source-map": "^2.0.0", "debug": "^4.1.0", "gensync": "^1.0.0-beta.2", @@ -146,16 +125,16 @@ } }, "node_modules/@babel/generator": { - "version": "7.27.0", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.27.0.tgz", - "integrity": "sha512-VybsKvpiN1gU1sdMZIp7FcqphVVKEwcuj02x73uvcHE0PTihx1nlBcowYWhDwjpoAXRv43+gDzyggGnn1XZhVw==", + "version": "7.28.3", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.3.tgz", + "integrity": "sha512-3lSpxGgvnmZznmBkCRnVREPUFJv2wrv9iAoFDvADJc0ypmdOxdUtcLeBgBJ6zE0PMeTKnxeQzyk0xTBq4Ep7zw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/parser": "^7.27.0", - "@babel/types": "^7.27.0", - "@jridgewell/gen-mapping": "^0.3.5", - "@jridgewell/trace-mapping": "^0.3.25", + "@babel/parser": "^7.28.3", + "@babel/types": "^7.28.2", + "@jridgewell/gen-mapping": "^0.3.12", + "@jridgewell/trace-mapping": "^0.3.28", "jsesc": "^3.0.2" }, "engines": { @@ -163,14 +142,14 @@ } }, "node_modules/@babel/helper-compilation-targets": { - "version": "7.27.0", - "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.27.0.tgz", - "integrity": "sha512-LVk7fbXml0H2xH34dFzKQ7TDZ2G4/rVTOrq9V+icbbadjbVxxeFeDsNHv2SrZeWoA+6ZiTyWYWtScEIW07EAcA==", + "version": "7.27.2", + "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.27.2.tgz", + "integrity": "sha512-2+1thGUUWWjLTYTHZWK1n8Yga0ijBz1XAhUXcKy81rd5g6yh7hGqMp45v7cadSbEHc9G3OTv45SyneRN3ps4DQ==", "dev": true, "license": "MIT", "dependencies": { - "@babel/compat-data": "^7.26.8", - "@babel/helper-validator-option": "^7.25.9", + "@babel/compat-data": "^7.27.2", + "@babel/helper-validator-option": "^7.27.1", "browserslist": "^4.24.0", "lru-cache": "^5.1.1", "semver": "^6.3.1" @@ -189,30 +168,40 @@ "semver": "bin/semver.js" } }, + "node_modules/@babel/helper-globals": { + "version": "7.28.0", + "resolved": "https://registry.npmjs.org/@babel/helper-globals/-/helper-globals-7.28.0.tgz", + "integrity": "sha512-+W6cISkXFa1jXsDEdYA8HeevQT/FULhxzR99pxphltZcVaugps53THCeiWA8SguxxpSp3gKPiuYfSWopkLQ4hw==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=6.9.0" + } + }, "node_modules/@babel/helper-module-imports": { - "version": "7.25.9", - "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.25.9.tgz", - "integrity": "sha512-tnUA4RsrmflIM6W6RFTLFSXITtl0wKjgpnLgXyowocVPrbYrLUXSBXDgTs8BlbmIzIdlBySRQjINYs2BAkiLtw==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.27.1.tgz", + "integrity": "sha512-0gSFWUPNXNopqtIPQvlD5WgXYI5GY2kP2cCvoT8kczjbfcfuIljTbcWrulD1CIPIX2gt1wghbDy08yE1p+/r3w==", "dev": true, "license": "MIT", "dependencies": { - "@babel/traverse": "^7.25.9", - "@babel/types": "^7.25.9" + "@babel/traverse": "^7.27.1", + "@babel/types": "^7.27.1" }, "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/helper-module-transforms": { - "version": "7.26.0", - "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.26.0.tgz", - "integrity": "sha512-xO+xu6B5K2czEnQye6BHA7DolFFmS3LB7stHZFaOLb1pAwO1HWLS8fXA+eh0A2yIvltPVmx3eNNDBJA2SLHXFw==", + "version": "7.28.3", + "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.28.3.tgz", + "integrity": "sha512-gytXUbs8k2sXS9PnQptz5o0QnpLL51SwASIORY6XaBKF88nsOT0Zw9szLqlSGQDP/4TljBAD5y98p2U1fqkdsw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-module-imports": "^7.25.9", - "@babel/helper-validator-identifier": "^7.25.9", - "@babel/traverse": "^7.25.9" + "@babel/helper-module-imports": "^7.27.1", + "@babel/helper-validator-identifier": "^7.27.1", + "@babel/traverse": "^7.28.3" }, "engines": { "node": ">=6.9.0" @@ -222,9 +211,9 @@ } }, "node_modules/@babel/helper-plugin-utils": { - "version": "7.26.5", - "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.26.5.tgz", - "integrity": "sha512-RS+jZcRdZdRFzMyr+wcsaqOmld1/EqTghfaBGQQd/WnRdzdlvSZ//kF7U8VQTxf1ynZ4cjUcYgjVGx13ewNPMg==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.27.1.tgz", + "integrity": "sha512-1gn1Up5YXka3YYAHGKpbideQ5Yjf1tDa9qYcgysz+cNCXukyLl6DjPXhD3VRwSb8c0J9tA4b2+rHEZtc6R0tlw==", "dev": true, "license": "MIT", "engines": { @@ -232,9 +221,9 @@ } }, "node_modules/@babel/helper-string-parser": { - "version": "7.25.9", - "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.25.9.tgz", - "integrity": "sha512-4A/SCr/2KLd5jrtOMFzaKjVtAei3+2r/NChoBNoZ3EyP/+GlhoaEGoWOZUmFmoITP7zOJyHIMm+DYRd8o3PvHA==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.27.1.tgz", + "integrity": 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"version": "9.0.0", - "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.0.tgz", - "integrity": "sha512-G8ura3S+3Z2G+mkgNRq8dqaFZAuxfsxpBB8OCTGRTCtp+l/v9nbFNmCUP1BZMts3G1142MsZfn6eeUKrr4PD1Q==", + "version": "9.0.2", + "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.2.tgz", + "integrity": "sha512-42AtmgqjV+X1VpdOfyTGOYRi0/zsoLqtXQckTmqTeybT+BDIbM/Guxo7x3pE2vtpr1ok6xRqM9OpBe+Jyoqyww==", + "license": "MIT", "peer": true, "dependencies": { "ansi-styles": "^6.2.1", @@ -5943,9 +7577,10 @@ } }, "node_modules/wrap-ansi/node_modules/ansi-regex": { - "version": "6.1.0", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.1.0.tgz", - "integrity": "sha512-7HSX4QQb4CspciLpVFwyRe79O3xsIZDDLER21kERQ71oaPodF8jL725AgJMFAYbooIqolJoRLuM81SpeUkpkvA==", + "version": "6.2.2", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.2.2.tgz", + "integrity": "sha512-Bq3SmSpyFHaWjPk8If9yc6svM8c56dB5BAtW4Qbw5jHTwwXXcTLoRMkpDJp6VL0XzlWaCHTXrkFURMYmD0sLqg==", + "license": "MIT", "peer": true, "engines": { "node": ">=12" @@ -5954,10 +7589,24 @@ "url": "https://github.com/chalk/ansi-regex?sponsor=1" } }, + "node_modules/wrap-ansi/node_modules/ansi-styles": { + "version": "6.2.3", + "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.3.tgz", + "integrity": "sha512-4Dj6M28JB+oAH8kFkTLUo+a2jwOFkuqb3yucU0CANcRRUbxS0cP0nZYCGjcc3BNXwRIsUVmDGgzawme7zvJHvg==", + "license": "MIT", + "peer": true, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/ansi-styles?sponsor=1" + } + }, "node_modules/wrap-ansi/node_modules/strip-ansi": { - "version": "7.1.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", - "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==", + "version": "7.1.2", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.2.tgz", + "integrity": "sha512-gmBGslpoQJtgnMAvOVqGZpEz9dyoKTCzy2nfz/n8aIFhN/jCE/rCmcxabB6jOOHV+0WNnylOxaxBQPSvcWklhA==", + "license": "MIT", "peer": true, "dependencies": { "ansi-regex": "^6.0.1" @@ -5973,12 +7622,14 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", - "dev": true + "dev": true, + "license": "ISC" }, "node_modules/y18n": { "version": "5.0.8", "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", + "license": "ISC", "peer": true, "engines": { "node": ">=10" @@ -5995,6 +7646,7 @@ "version": "18.0.0", "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.0.0.tgz", "integrity": "sha512-4UEqdc2RYGHZc7Doyqkrqiln3p9X2DZVxaGbwhn2pi7MrRagKaOcIKe8L3OxYcbhXLgLFUS3zAYuQjKBQgmuNg==", + "license": "MIT", "peer": true, "dependencies": { "cliui": "^9.0.1", @@ -6012,6 +7664,7 @@ "version": "22.0.0", "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-22.0.0.tgz", "integrity": "sha512-rwu/ClNdSMpkSrUb+d6BRsSkLUq1fmfsY6TOpYzTwvwkg1/NRG85KBy3kq++A8LKQwX6lsu+aWad+2khvuXrqw==", + "license": "ISC", "peer": true, "engines": { "node": "^20.19.0 || ^22.12.0 || >=23" @@ -6022,6 +7675,7 @@ "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", "dev": true, + "license": "MIT", "engines": { "node": ">=10" }, @@ -6033,6 +7687,7 @@ "version": "2.0.4", "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz", "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==", + "license": "MIT", "funding": { "type": "github", "url": "https://github.com/sponsors/wooorm" diff --git a/ui/package.json b/ui/package.json index 7ccc253f..78ba8c5f 100644 --- a/ui/package.json +++ b/ui/package.json @@ -12,6 +12,7 @@ "generate-types-local": "npx openapi-typescript http://localhost:8000/openapi.json -o bedbase-types.d.ts" }, "dependencies": { + "@databio/gtars": "file:../../gtars/gtars-wasm/pkg", "@tanstack/react-query": "^5.28.0", "@tanstack/react-query-devtools": "^5.28.0", "@tanstack/react-table": "^8.15.3", @@ -23,7 +24,6 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", - "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", "pako": "^2.1.0", "react": "^18.2.0", @@ -38,7 +38,9 @@ "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", "three": "^0.177.0", - "vega-embed": "^7.0.2" + "vega-embed": "^7.0.2", + "vite-plugin-top-level-await": "^1.6.0", + "vite-plugin-wasm": "^3.5.0" }, "devDependencies": { "@types/js-yaml": "^4.0.9", diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index c9e661eb..83100862 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -1,6 +1,6 @@ import { useState, useRef } from 'react'; import { Layout } from '../components/layout.tsx'; -import { RegionSet } from 'gtars-js'; +import { RegionSet } from '@databio/gtars'; import { handleBedFileInput, type BedEntry } from '../utils.ts'; export const BEDAnalytics = () => { diff --git a/ui/vite.config.ts b/ui/vite.config.ts index 5a33944a..443bb22f 100644 --- a/ui/vite.config.ts +++ b/ui/vite.config.ts @@ -1,7 +1,17 @@ import { defineConfig } from 'vite' import react from '@vitejs/plugin-react' +import topLevelAwait from 'vite-plugin-top-level-await'; +import wasm from 'vite-plugin-wasm'; // https://vitejs.dev/config/ export default defineConfig({ - plugins: [react()], + plugins: [wasm(), topLevelAwait(), react()], + build: { + target: 'esnext', // Ensure ESNext target for WASM support + }, + server: { + fs: { + allow: ['..'], // Allow serving files from one level up to the project root + }, + }, }) From 9b31bac1e7b4e0b88cac831def86b39d1b01ec9a Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 16 Oct 2025 16:56:01 -0400 Subject: [PATCH 03/65] add loading sign --- ui/src/pages/bed-analytics.tsx | 79 ++++++++++++++++++++++++---------- 1 file changed, 56 insertions(+), 23 deletions(-) diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 83100862..79169efe 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -8,15 +8,27 @@ export const BEDAnalytics = () => { const [Rs, setRs] = useState(null); const [loadingRS, setLoadingRS] = useState(false); const regionsetFileInputRef = useRef(null); + const [processingTime, setProcessingTime] = useState(null); - const initializeRegionSet = (regionsetRegions) => { + const initializeRegionSet = async (regionsetRegions: BedEntry[] | null) => { if (regionsetRegions) { console.log('initializing regionset'); console.log(regionsetRegions); setLoadingRS(true); - const rs = new RegionSet(regionsetRegions); - setRs(rs); - setLoadingRS(false); + setProcessingTime(null); + + // Use setTimeout to allow the UI to update before processing + setTimeout(() => { + const startTime = performance.now(); + const rs = new RegionSet(regionsetRegions); + const endTime = performance.now(); + const processingTimeMs = endTime - startTime; + + console.log(rs.digest()); + setRs(rs); + setProcessingTime(processingTimeMs); + setLoadingRS(false); + }, 10); } else { setLoadingRS(false); } @@ -24,16 +36,17 @@ export const BEDAnalytics = () => { return ( -
+

BED analyzer

+
- + { @@ -49,26 +62,21 @@ export const BEDAnalytics = () => { /> {regionsetRegions && (

- {regionsetRegions.length} regions in universe + {regionsetRegions.length} regions in provided BED file

)}
-
- {Rs &&

RegionSet initialized with {Rs.get_phi} regions

} -
- -
+
-
+ {loadingRS && (
- - RegionSet ready - -
+ className="d-inline-flex align-items-center gap-2 px-3 py-2 bg-success bg-opacity-10 border border-success border-opacity-25 rounded-pill"> +
+ Loading... +
+ + Analyzing RegionSet... + +
+ )} + + {Rs && !loadingRS && ( +
+
+ + Results ready + +
+ )} +
{Rs && (

Mean region width: {Rs.mean_region_width}

Total number of regions: {Rs.number_of_regions}

Total number of nucleotides: {Rs.total_nucleotides}

+

Identifier: {Rs.digest()}

+ {processingTime !== null && ( +

Processing time: {(processingTime / 1000).toFixed(3)} seconds

+ )}
)}
From b82c8a92eccfbbe1cf863ec9693ef124416fbf90 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 16 Oct 2025 17:25:30 -0400 Subject: [PATCH 04/65] more ui bedqc improvements --- ui/src/pages/bed-analytics.tsx | 117 +++++++++++++++++++++------------ 1 file changed, 74 insertions(+), 43 deletions(-) diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 79169efe..a6dfbb0c 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -7,30 +7,43 @@ export const BEDAnalytics = () => { const [regionsetRegions, setregionsetRegions] = useState(null); const [Rs, setRs] = useState(null); const [loadingRS, setLoadingRS] = useState(false); - const regionsetFileInputRef = useRef(null); - const [processingTime, setProcessingTime] = useState(null); + const regionsetFileInputRef = useRef(null); + const [totalProcessingTime, setTotalProcessingTime] = useState(null); + const [selectedFile, setSelectedFile] = useState(null); - const initializeRegionSet = async (regionsetRegions: BedEntry[] | null) => { - if (regionsetRegions) { - console.log('initializing regionset'); - console.log(regionsetRegions); + const initializeRegionSet = async () => { + if (selectedFile) { setLoadingRS(true); - setProcessingTime(null); + setTotalProcessingTime(null); - // Use setTimeout to allow the UI to update before processing - setTimeout(() => { + try { + // Start timing from the beginning of file loading const startTime = performance.now(); - const rs = new RegionSet(regionsetRegions); - const endTime = performance.now(); - const processingTimeMs = endTime - startTime; - console.log(rs.digest()); - setRs(rs); - setProcessingTime(processingTimeMs); + // Create a synthetic event for handleBedFileInput + const syntheticEvent = { + target: { files: [selectedFile] }, + } as unknown as Event; + + await handleBedFileInput(syntheticEvent, (entries) => { + setregionsetRegions(entries); + + // Process the RegionSet immediately after loading + setTimeout(() => { + const rs = new RegionSet(entries); + const endTime = performance.now(); + const totalTimeMs = endTime - startTime; + + console.log(rs.digest()); + setRs(rs); + setTotalProcessingTime(totalTimeMs); + setLoadingRS(false); + }, 10); + }); + } catch (error) { setLoadingRS(false); - }, 10); - } else { - setLoadingRS(false); + console.error('Error loading file:', error); + } } }; @@ -50,42 +63,41 @@ export const BEDAnalytics = () => { }} type="file" onChange={(e) => { - const input = e.target as HTMLInputElement; - const file = input.files?.[0]; + const file = e.target.files?.[0]; if (file) { - // @ts-expect-error its fine :) - handleBedFileInput(e, (entries) => { - setregionsetRegions(entries); - }); + setSelectedFile(file); } }} /> + {selectedFile && ( +

+ Selected file: {selectedFile.name} +

+ )} {regionsetRegions && (

- {regionsetRegions.length} regions in provided BED file + {regionsetRegions.length} regions loaded from BED file

)}
- Analyzing RegionSet... - + Loading and analyzing... +
)} @@ -120,21 +132,40 @@ export const BEDAnalytics = () => { style={{ width: '8px', height: '8px' }} /> - Results ready - + Results ready +
)}
{Rs && (
-

Mean region width: {Rs.mean_region_width}

-

Total number of regions: {Rs.number_of_regions}

-

Total number of nucleotides: {Rs.total_nucleotides}

-

Identifier: {Rs.digest()}

- {processingTime !== null && ( -

Processing time: {(processingTime / 1000).toFixed(3)} seconds

- )} + + + + + + + + + + + + + + + + + + + {totalProcessingTime !== null && ( + + + + + )} + +
Mean region width{Rs.mean_region_width}
Total number of regions{Rs.number_of_regions}
Total number of nucleotides{Rs.total_nucleotides}
Identifier{Rs.digest()}
Total processing time{(totalProcessingTime / 1000).toFixed(3)} seconds
)}
From cf727212848eb672e11b2036a7825a28d83e326b Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Sun, 19 Oct 2025 23:38:19 -0400 Subject: [PATCH 05/65] added more statistics --- .../chromosome-stats-panel.tsx | 148 ++++++++++++++++++ ui/src/pages/bed-analytics.tsx | 82 ++++++---- 2 files changed, 196 insertions(+), 34 deletions(-) create mode 100644 ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx new file mode 100644 index 00000000..28f5d981 --- /dev/null +++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx @@ -0,0 +1,148 @@ +import React from 'react'; +import { ChromosomeStats, RegionSet } from '@databio/gtars'; + +interface Props { + Rs: RegionSet; + selectedFile: File | null; +} + +const ChromosomeStatsPanel: React.FC = ({ Rs, selectedFile }) => { + const calc = Rs.calculate_statistics?.(); + if (!calc) return null; + + const statsEntries = Array.from(calc.entries()) + .map(([chrom, stats]: [unknown, ChromosomeStats]) => { + const cs = stats as ChromosomeStats; + const row = { + chromosome: String(chrom), + count: cs.count, + minimum: cs.minimum, + maximum: cs.maximum, + mean: cs.mean.toFixed(2), + median: cs.median.toFixed(2), + start: cs.start, + end: cs.end, + }; + try { + (cs as unknown as { free?: () => void }).free?.(); + } catch (e) { + /* ignore */ + } + return row; + }) + .sort((a, b) => + a.chromosome.localeCompare(b.chromosome, undefined, { + numeric: true, + sensitivity: 'base', + }), + ); + + return ( +
+
+
Number of regions per chromosome:
+
+ + {(() => { + const barWidth = 36; + const gap = 24; + const maxCount = Math.max(...statsEntries.map(s => s.count), 1); + const chartHeight = 100; + return statsEntries.map((s, i) => { + const x = i * (barWidth + gap) + 16; + const barH = Math.round((s.count / maxCount) * chartHeight); + const y = 20 + (chartHeight - barH); + return ( + + + + {s.count} + + + {s.chromosome} + + + ); + }); + })()} + + +
+
+ +
+
+
+
Chromosome regions statatistics
+
+ +
+
+ + + + + + + + + + + + + + + + {statsEntries.map((s) => ( + + + + + + + + + + + ))} + +
ChromosomeCountStartEndMinMaxMeanMedian
{s.chromosome}{s.count}{s.start}{s.end}{s.minimum}{s.maximum}{s.mean}{s.median}
+
+
+
+ ); +}; + +export default ChromosomeStatsPanel; \ No newline at end of file diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index a6dfbb0c..57429e61 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -1,7 +1,8 @@ import { useState, useRef } from 'react'; import { Layout } from '../components/layout.tsx'; -import { RegionSet } from '@databio/gtars'; +import { RegionSet, ChromosomeStats } from '@databio/gtars'; import { handleBedFileInput, type BedEntry } from '../utils.ts'; +import ChromosomeStatsPanel from '../components/bed-analytics-components/chromosome-stats-panel.tsx'; export const BEDAnalytics = () => { const [regionsetRegions, setregionsetRegions] = useState(null); @@ -11,6 +12,15 @@ export const BEDAnalytics = () => { const [totalProcessingTime, setTotalProcessingTime] = useState(null); const [selectedFile, setSelectedFile] = useState(null); + + const formatFileSize = (bytes: number): string => { + if (bytes === 0) return '0 B'; + const k = 1024; + const sizes = ['B', 'KB', 'MB', 'GB']; + const i = Math.floor(Math.log(bytes) / Math.log(k)); + return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i]; + }; + const initializeRegionSet = async () => { if (selectedFile) { setLoadingRS(true); @@ -34,7 +44,7 @@ export const BEDAnalytics = () => { const endTime = performance.now(); const totalTimeMs = endTime - startTime; - console.log(rs.digest()); + console.log(rs.digest); setRs(rs); setTotalProcessingTime(totalTimeMs); setLoadingRS(false); @@ -65,19 +75,22 @@ export const BEDAnalytics = () => { onChange={(e) => { const file = e.target.files?.[0]; if (file) { + // unload any previous results when a new file is selected + setRs(null); + setregionsetRegions(null); + setTotalProcessingTime(null); setSelectedFile(file); } }} /> {selectedFile && ( -

- Selected file: {selectedFile.name} -

- )} - {regionsetRegions && ( -

- {regionsetRegions.length} regions loaded from BED file -

+
+
Selected file: {selectedFile.name}
+
File size: {formatFileSize(selectedFile.size)}
+ {Rs && totalProcessingTime !== null && ( +
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s
+ )} +
)}
@@ -140,32 +153,33 @@ export const BEDAnalytics = () => {
{Rs && (
- - - - - - - - - - - - - - - - - - - {totalProcessingTime !== null && ( +
+
Mean region width{Rs.mean_region_width}
Total number of regions{Rs.number_of_regions}
Total number of nucleotides{Rs.total_nucleotides}
Identifier{Rs.digest()}
+ + + + + + + + + - - + + - )} - -
Identifier{Rs.digest}
Mean region width{Rs.mean_region_width}
Total processing time{(totalProcessingTime / 1000).toFixed(3)} secondsTotal number of regions{Rs.number_of_regions}
+ + Total number of nucleotides + {Rs.total_nucleotides} + + + +
+
+

Interval chromosome length statistics

+ + {Rs.calculate_statistics && } +
)} From ceece9d3f40a64959d26c7b98325b260d64d60c7 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Mon, 20 Oct 2025 00:02:52 -0400 Subject: [PATCH 06/65] Added url as input option --- ui/src/pages/bed-analytics.tsx | 189 ++++++++++++++++++++++----------- 1 file changed, 129 insertions(+), 60 deletions(-) diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 57429e61..02614b3b 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -11,7 +11,8 @@ export const BEDAnalytics = () => { const regionsetFileInputRef = useRef(null); const [totalProcessingTime, setTotalProcessingTime] = useState(null); const [selectedFile, setSelectedFile] = useState(null); - + const [inputMode, setInputMode] = useState<'file' | 'url'>('file'); + const [bedUrl, setBedUrl] = useState(''); const formatFileSize = (bytes: number): string => { if (bytes === 0) return '0 B'; @@ -21,24 +22,44 @@ export const BEDAnalytics = () => { return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i]; }; + const fetchBedFromUrl = async (url: string): Promise => { + const response = await fetch(url); + if (!response.ok) { + throw new Error(`Failed to fetch BED file: ${response.statusText}`); + } + const blob = await response.blob(); + const fileName = url.split('/').pop() || 'remote-bed-file.bed'; + return new File([blob], fileName, { type: 'text/plain' }); + }; + const initializeRegionSet = async () => { - if (selectedFile) { + let fileToProcess: File | null = null; + + if (inputMode === 'file' && selectedFile) { + fileToProcess = selectedFile; + } else if (inputMode === 'url' && bedUrl.trim()) { + try { + fileToProcess = await fetchBedFromUrl(bedUrl.trim()); + } catch (error) { + console.error('Error fetching URL:', error); + return; + } + } + + if (fileToProcess) { setLoadingRS(true); setTotalProcessingTime(null); try { - // Start timing from the beginning of file loading const startTime = performance.now(); - // Create a synthetic event for handleBedFileInput const syntheticEvent = { - target: { files: [selectedFile] }, + target: { files: [fileToProcess] }, } as unknown as Event; await handleBedFileInput(syntheticEvent, (entries) => { setregionsetRegions(entries); - // Process the RegionSet immediately after loading setTimeout(() => { const rs = new RegionSet(entries); const endTime = performance.now(); @@ -57,64 +78,118 @@ export const BEDAnalytics = () => { } }; + const clearAll = () => { + setRs(null); + setregionsetRegions(null); + setTotalProcessingTime(null); + setSelectedFile(null); + setBedUrl(''); + if (regionsetFileInputRef.current) { + regionsetFileInputRef.current.value = ''; + } + }; + return (

BED analyzer

-
- - { - const file = e.target.files?.[0]; - if (file) { - // unload any previous results when a new file is selected - setRs(null); - setregionsetRegions(null); - setTotalProcessingTime(null); - setSelectedFile(file); - } - }} - /> - {selectedFile && ( -
-
Selected file: {selectedFile.name}
-
File size: {formatFileSize(selectedFile.size)}
- {Rs && totalProcessingTime !== null && ( -
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s
+
+
+
+ setInputMode('file')} + /> + +
+
+ setInputMode('url')} + /> + +
+
+ + {inputMode === 'file' ? ( +
+ + { + const file = e.target.files?.[0]; + if (file) { + clearAll(); + setSelectedFile(file); + } + }} + /> + {selectedFile && ( +
+
Selected file: {selectedFile.name}
+
File size: {formatFileSize(selectedFile.size)}
+
+ )} +
+ ) : ( +
+ + { + setBedUrl(e.target.value); + if (Rs) clearAll(); + }} + /> + {bedUrl && ( +
+ URL: {bedUrl} +
)}
)} + + {Rs && totalProcessingTime !== null && ( +
+ Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s +
+ )}
-
+
@@ -124,11 +199,7 @@ export const BEDAnalytics = () => { {loadingRS && (
-
+
Loading...
@@ -140,10 +211,7 @@ export const BEDAnalytics = () => { {Rs && !loadingRS && (
-
+
Results ready @@ -166,7 +234,7 @@ export const BEDAnalytics = () => { Total number of regions - {Rs.number_of_regions} + {Rs.total_nucleotides} Total number of nucleotides @@ -177,8 +245,9 @@ export const BEDAnalytics = () => {

Interval chromosome length statistics

- - {Rs.calculate_statistics && } + {Rs.calculate_statistics && ( + + )}
)} From 4f248ffddca7a34a77da18db72dcccd20a5c2e33 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 21 Oct 2025 04:53:11 +0000 Subject: [PATCH 07/65] Bump vite from 6.3.6 to 6.4.1 in /ui Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 6.3.6 to 6.4.1. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/main/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/create-vite@6.4.1/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 6.4.1 dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- ui/package-lock.json | 9 +++++---- ui/package.json | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index 463ba7ef..2d032b5c 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -47,7 +47,7 @@ "eslint-plugin-react-refresh": "^0.4.5", "sass": "^1.72.0", "typescript": "^5.2.2", - "vite": "^6.3.6" + "vite": "^6.4.1" } }, "node_modules/@aashutoshrathi/word-wrap": { @@ -5963,10 +5963,11 @@ } }, "node_modules/vite": { - "version": "6.3.6", - "resolved": "https://registry.npmjs.org/vite/-/vite-6.3.6.tgz", - "integrity": "sha512-0msEVHJEScQbhkbVTb/4iHZdJ6SXp/AvxL2sjwYQFfBqleHtnCqv1J3sa9zbWz/6kW1m9Tfzn92vW+kZ1WV6QA==", + "version": "6.4.1", + "resolved": "https://registry.npmjs.org/vite/-/vite-6.4.1.tgz", + "integrity": "sha512-+Oxm7q9hDoLMyJOYfUYBuHQo+dkAloi33apOPP56pzj+vsdJDzr+j1NISE5pyaAuKL4A3UD34qd0lx5+kfKp2g==", "dev": true, + "license": "MIT", "dependencies": { "esbuild": "^0.25.0", "fdir": "^6.4.4", diff --git a/ui/package.json b/ui/package.json index 8cd690a3..a33e10af 100644 --- a/ui/package.json +++ b/ui/package.json @@ -51,6 +51,6 @@ "eslint-plugin-react-refresh": "^0.4.5", "sass": "^1.72.0", "typescript": "^5.2.2", - "vite": "^6.3.6" + "vite": "^6.4.1" } } From 7e7fecb24de75a96625a79241825340b46295c5a Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 24 Oct 2025 14:48:42 -0400 Subject: [PATCH 08/65] ui cleanup --- .../cards/stat-card-wrapper.tsx | 15 ++++------ .../charts/genomic-feature-bar.tsx | 7 ++++- .../bed-splash-components/header.tsx | 5 ++-- .../bed-splash-components/plots.tsx | 13 ++++---- .../bed-splash-components/refgenome-modal.tsx | 4 +-- .../bedset-splash-components/beds-table.tsx | 2 +- .../cards/gc-content-card.tsx | 8 ++--- .../cards/median-region-width.tsx | 7 ++--- .../cards/median-tss-distance.tsx | 7 ++--- .../cards/stat-card-wrapper.tsx | 15 ++++------ .../charts/genomic-feature-bar.tsx | 10 ++++--- .../bedset-splash-components/header.tsx | 15 +++++----- .../bedset-splash-components/plots.tsx | 10 +++---- ui/src/components/nav/nav-desktop.tsx | 17 +++++------ ui/src/components/nav/nav-logo.tsx | 4 +-- .../text2bed/t2b-search-results-table.tsx | 2 +- ui/src/custom.scss | 6 ++-- ui/src/pages/bed-splash.tsx | 30 +++++++++---------- ui/src/pages/bedset-splash.tsx | 20 ++++++------- ui/src/pages/metrics.tsx | 2 -- ui/src/queries/useText2BedSearch.ts | 1 - ui/src/utils.ts | 8 +++++ 22 files changed, 101 insertions(+), 107 deletions(-) diff --git a/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx b/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx index 7b1b5b46..0fd96d5b 100644 --- a/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx +++ b/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx @@ -12,18 +12,15 @@ export const StatCard = (props: Props) => { const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( +
-
-

{title}

-
-

{stat}

-
-
- - - +
+
{title}
+
+

{stat}

+ ); }; diff --git a/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx index 59342828..c3a65988 100644 --- a/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx @@ -24,6 +24,11 @@ const chartOptions = { display: false, }, }, + layout: { + padding: { + bottom: 25 + } + } }; export const GenomicFeatureBar = (props: Props) => { @@ -98,7 +103,7 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
+

Genomic Features

diff --git a/ui/src/components/bed-splash-components/header.tsx b/ui/src/components/bed-splash-components/header.tsx index 7a04d4a1..5bf6c884 100644 --- a/ui/src/components/bed-splash-components/header.tsx +++ b/ui/src/components/bed-splash-components/header.tsx @@ -35,7 +35,6 @@ export const BedSplashHeader = (props: Props) => {

- {metadata?.id || 'No ID available'}

-
{metadata.name}
-

{metadata?.description || 'No description available'}

+
{metadata.name}
+

{metadata?.description || 'No description available'}

diff --git a/ui/src/components/bed-splash-components/plots.tsx b/ui/src/components/bed-splash-components/plots.tsx index d04546ee..3680d1db 100644 --- a/ui/src/components/bed-splash-components/plots.tsx +++ b/ui/src/components/bed-splash-components/plots.tsx @@ -30,16 +30,16 @@ const Plot = (props: PlotProps) => { setShow(true); } }} - className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all" + className="h-100 border rounded p-2 shadow-sm hover-border-primary transition-all" > -
- {title} +
+

{title}

{/* */}
- {alt} + {alt}
{ export const Plots = (props: PlotsProps) => { const { metadata } = props; - const plotNames = metadata.plots ? Object.keys(metadata.plots) : []; + // comment out partitions because we already have it in statistics section + const plotNames = metadata.plots ? Object.keys(metadata.plots).filter((name: string) => name != 'partitions') : []; return ( - + {metadata.plots && chunkArray(plotNames, 3).map((chunk, idx) => ( diff --git a/ui/src/components/bed-splash-components/refgenome-modal.tsx b/ui/src/components/bed-splash-components/refgenome-modal.tsx index e240530f..65cc4cec 100644 --- a/ui/src/components/bed-splash-components/refgenome-modal.tsx +++ b/ui/src/components/bed-splash-components/refgenome-modal.tsx @@ -13,8 +13,6 @@ type Props = { export const RefGenomeModal = (props: Props) => { const { show, onHide, genomeStats } = props; - console.log(genomeStats?.compared_genome) - return ( { ) .map(genome => ( { />
- +
{table.getHeaderGroups().map((headerGroup) => ( diff --git a/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx b/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx index 9983fccd..61b1bbf2 100644 --- a/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx +++ b/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx @@ -13,13 +13,11 @@ export const GCContentCard = (props: Props) => { return (
-

+

{metadata.statistics?.mean?.gc_content ? `${formatNumberWithCommas(Math.round((metadata.statistics?.mean?.gc_content || 0)*100)/100)}` - : 'N/A'} -

- {/* plus minus */} -

± {formatNumberWithCommas(Math.round((metadata.statistics?.sd?.gc_content || 0)*100)/100)}

+ : 'N/A'} {' '} ± {formatNumberWithCommas(Math.round((metadata.statistics?.sd?.gc_content || 0)*100)/100)} +
); diff --git a/ui/src/components/bedset-splash-components/cards/median-region-width.tsx b/ui/src/components/bedset-splash-components/cards/median-region-width.tsx index b198fec2..7337d426 100644 --- a/ui/src/components/bedset-splash-components/cards/median-region-width.tsx +++ b/ui/src/components/bedset-splash-components/cards/median-region-width.tsx @@ -13,11 +13,8 @@ export const MeanRegionWidthCard = (props: Props) => { return (
-

- {formatNumberWithCommas(Math.round(metadata.statistics?.mean?.mean_region_width || 0))} bp -

- {/* plus minus */} -

+

+ {formatNumberWithCommas(Math.round(metadata.statistics?.mean?.mean_region_width || 0))} {' '} ± {formatNumberWithCommas(Math.round(metadata.statistics?.sd?.mean_region_width || 0))} bp

diff --git a/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx b/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx index 62cb1347..ac2e61f9 100644 --- a/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx +++ b/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx @@ -15,11 +15,8 @@ export const MedianTssDistCard = (props: Props) => { tooltip="The median distance of the regions to the nearest transcription start site." >
-

- {formatNumberWithCommas(Math.round(metadata?.statistics?.mean?.median_tss_dist || 0))} bp -

- {/* plus minus */} -

+

+ {formatNumberWithCommas(Math.round(metadata?.statistics?.mean?.median_tss_dist || 0))} {' '} ± {formatNumberWithCommas(Math.round(metadata?.statistics?.sd?.median_tss_dist || 0))} bp

diff --git a/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx b/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx index 34daf17e..fc51cc25 100644 --- a/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx +++ b/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx @@ -11,16 +11,13 @@ export const StatCard = (props: Props) => { const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( -
-
-

{title}

-
{children}
-
- - - + +
+
+
{title}
+
{children}
-
+ ); }; diff --git a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx index fd445c82..c820a99e 100644 --- a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx @@ -33,6 +33,11 @@ const chartOptions = { display: false, }, }, + layout: { + padding: { + bottom: 25 + } + } }; export const GenomicFeatureBar = (props: Props) => { @@ -188,7 +193,7 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
+

Genomic Features

@@ -235,9 +240,6 @@ export const GenomicFeatureBar = (props: Props) => { }} />
-
-

Learn more

-
); diff --git a/ui/src/components/bedset-splash-components/header.tsx b/ui/src/components/bedset-splash-components/header.tsx index c33a1fb8..2896c572 100644 --- a/ui/src/components/bedset-splash-components/header.tsx +++ b/ui/src/components/bedset-splash-components/header.tsx @@ -30,7 +30,6 @@ export const BedsetSplashHeader = (props: Props) => {

- {metadata?.id || 'No name available'}

-

{metadata?.description || 'No description available'}

+

{metadata?.description || 'No description available'}

Author: {metadata?.author || 'None'}

-

Source: {metadata?.source || 'None'}

+

Source: {metadata?.source || 'None'}

-
-
+
+

-

+
{metadata.md5sum}

{metadata.bed_ids && (

-

+
{metadata.bed_ids?.length} BED files
@@ -152,7 +151,7 @@ export const BedsetSplashHeader = (props: Props) => {
+ className="d-flex flex-column flex-md-row justify-content-xl-between align-items-start align-items-xl-end text-sm">

diff --git a/ui/src/components/bedset-splash-components/plots.tsx b/ui/src/components/bedset-splash-components/plots.tsx index 4e2cdce3..86fddb90 100644 --- a/ui/src/components/bedset-splash-components/plots.tsx +++ b/ui/src/components/bedset-splash-components/plots.tsx @@ -31,14 +31,14 @@ const Plot = (props: PlotProps) => { }} className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all" > -

- {title} +
+ {title} {/* */}
-
- +
+
{ const plotNames = metadata.plots ? Object.keys(metadata.plots) : []; return ( - + {metadata.plots && chunkArray(plotNames, 3).map((chunk, idx) => ( diff --git a/ui/src/components/nav/nav-desktop.tsx b/ui/src/components/nav/nav-desktop.tsx index ab26e083..61b12094 100644 --- a/ui/src/components/nav/nav-desktop.tsx +++ b/ui/src/components/nav/nav-desktop.tsx @@ -6,28 +6,27 @@ export const NavDesktop = () => { const { cart } = useBedCart(); return (
- + diff --git a/ui/src/custom.scss b/ui/src/custom.scss index 4c40686a..eb74476a 100644 --- a/ui/src/custom.scss +++ b/ui/src/custom.scss @@ -98,15 +98,15 @@ a { } .bed-splash-genomic-feature-bar-height { - height: 27rem; + height: 26.375rem; } .bedset-splash-stat-card-height { - min-height: 7rem; + min-height: 9rem; } .bedset-splash-genomic-feature-bar-height { - height: 24rem; + height: 24.875rem; } .min-h-screen { diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 75f9521f..0618c31d 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -101,10 +101,10 @@ export const BedSplash = () => { >

Oh no!

-

+

We could not find BED with record identifier:
{bedId} -
+

@@ -141,9 +141,9 @@ export const BedSplash = () => { {metadata !== undefined ? : null} - -

-

Overview

+ + +
Overview
Name Genome Tissue
@@ -199,8 +199,8 @@ export const BedSplash = () => { - -

BEDsets

+ +
BEDsets
@@ -248,31 +248,31 @@ export const BedSplash = () => { - -

Statistics

+ +
Statistics
{metadata && ( - + )} - + - -

Plots

+ +
Plots
 {neighbours && ( - -

Similar BED Files

+ +
Similar BED Files
 diff --git a/ui/src/pages/bedset-splash.tsx b/ui/src/pages/bedset-splash.tsx index d7ffc5af..5b3500e2 100644 --- a/ui/src/pages/bedset-splash.tsx +++ b/ui/src/pages/bedset-splash.tsx @@ -71,10 +71,10 @@ export const BedsetSplash = () => { >

Oh no!

-

+

We could not find BEDset with record identifier:
{bedsetId} -
+

@@ -108,29 +108,29 @@ export const BedsetSplash = () => {

{(metadata !== undefined) && bedfiles ? : null} - -

Statistics

+ +
Statistics
{metadata && ( - + )} - + - + -

Plots

+
Plots
- -

Constituent BED Files

+ +
Constituent BED Files
{isLoadingBedfiles ? (
diff --git a/ui/src/pages/metrics.tsx b/ui/src/pages/metrics.tsx index b3d2757b..c524a755 100644 --- a/ui/src/pages/metrics.tsx +++ b/ui/src/pages/metrics.tsx @@ -73,8 +73,6 @@ export const Metrics = () => { const { data: detailedStats, isLoading: statsIsLoading } = useDetailedStats(); const { data: usageStats, isLoading: usageIsLoading } = useDetailedUsage(); - console.log(detailedStats); - if (statsIsLoading || usageIsLoading) { return ( diff --git a/ui/src/queries/useText2BedSearch.ts b/ui/src/queries/useText2BedSearch.ts index 229eb7e6..f469560c 100644 --- a/ui/src/queries/useText2BedSearch.ts +++ b/ui/src/queries/useText2BedSearch.ts @@ -21,7 +21,6 @@ export const useText2BedSearch = (query: SearchQuery) => { if (autoRun !== undefined && autoRun === true && !!q) { enabled = true; } - console.log(assay) return useQuery({ queryKey: ['search', q, limit, offset, genome, assay], queryFn: async () => { diff --git a/ui/src/utils.ts b/ui/src/utils.ts index 4cc01e5b..8baa86bd 100644 --- a/ui/src/utils.ts +++ b/ui/src/utils.ts @@ -118,6 +118,14 @@ export const snakeToTitleCase = (str: string) => { .join(' '); }; +export const toTitleCase = (str: string): string => { + return str + .toLowerCase() + .split(' ') + .map(word => word.charAt(0).toUpperCase() + word.slice(1)) + .join(' '); +} + export const convertStatusCodeToMessage = (statusCode: number | undefined) => { if (statusCode === undefined) { return 'Unknown Error'; From fe981301485530b5a757683b2d0f6a39b60c3a47 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Fri, 24 Oct 2025 16:56:13 -0400 Subject: [PATCH 09/65] Adding region distribution plot --- ui/package-lock.json | 2 +- .../bed-analytics-components/bed-plots.tsx | 123 ++++++++++++++++++ .../chromosome-stats-panel.tsx | 4 +- ui/src/main.tsx | 2 +- ui/src/pages/bed-analytics.tsx | 71 +++++----- 5 files changed, 168 insertions(+), 34 deletions(-) create mode 100644 ui/src/components/bed-analytics-components/bed-plots.tsx diff --git a/ui/package-lock.json b/ui/package-lock.json index 55c99c46..b80b72b1 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -56,7 +56,7 @@ }, "../../gtars/gtars-wasm/pkg": { "name": "@databio/gtars", - "version": "0.5.0" + "version": "0.5.1" }, "node_modules/@babel/code-frame": { "version": "7.27.1", diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx new file mode 100644 index 00000000..accb67ee --- /dev/null +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -0,0 +1,123 @@ +import { useEffect, useRef } from 'react'; +import embed from 'vega-embed'; + + +interface Props { + xlab?: string; + ylab?: string; + height?: number; + color?: number; + angle?: boolean; + maxLength?: number; +} + +const distributionSpec = (data: any, props: Props = {}) => { + const { xlab = 'Label', ylab = 'Value', height = 300, color = 0, angle = false, maxLength = 15 } = props; + + // Transform data to match the new schema requirements + const transformedData = data.map((item: any, index: number) => ({ + chr: item.chr, + withinGroupID: item.rid, + N: item.n, + start: item.start, + end: item.end, + })); + + return { + $schema: 'https://vega-github.io/schema/vega-lite/v6.json', + config: { + axis: { + grid: false, + }, + facet: { + spacing: -1, + }, + view: { + continuousHeight: 300, + continuousWidth: 300, + strokeWidth: 0, + cursor: 'inherit', + }, + }, + data: { + values: transformedData, + }, + encoding: { + row: { + field: 'chr', + header: { + labelAlign: 'right', + labelAngle: 0, + labelOrient: 'right', + labelPadding: 5, + }, + sort: [ + 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', + 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', + 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', + ], + title: 'Number of Regions', + type: 'ordinal', + }, + x: { + axis: { + // labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'', + values: [0, 300.0], + }, + field: 'withinGroupID', + scale: { + domain: [0, 300.0], + }, + title: 'Genome', + type: 'quantitative', + }, + y: { + axis: { + values: [10.0, 20.0, 30.0], + }, + field: 'N', + title: '', + type: 'quantitative', + }, + }, + height: 25, + mark: { + cornerRadiusEnd: 0.5, + type: 'bar', + width: 2.5, + }, + width: 750, + }; +}; + +export const ChromosomeBarPlot = (props: Props) => { + const { data, xlab, ylab, height, color, action } = props; + + const plotRef = useRef(null); + const spec = distributionSpec(data, { xlab, ylab, height, color }); + + useEffect(() => { + if (plotRef.current && spec) { + try { + embed(plotRef.current as HTMLDivElement, spec as any, { 'actions': action }) + .catch(error => { + console.error('Embed error after parsing:', error); + }); + } catch (error) { + console.error(error); + } + } + + return () => { + if (plotRef.current) { + plotRef.current.innerHTML = ''; + } + }; + }, [spec, action]); + + return ( +
+ ); +}; + +export default ChromosomeBarPlot; diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx index 28f5d981..50c3be5f 100644 --- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx +++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx @@ -6,8 +6,8 @@ interface Props { selectedFile: File | null; } -const ChromosomeStatsPanel: React.FC = ({ Rs, selectedFile }) => { - const calc = Rs.calculate_statistics?.(); +const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => { + const calc = rs.calculate_statistics?.(); if (!calc) return null; const statsEntries = Array.from(calc.entries()) diff --git a/ui/src/main.tsx b/ui/src/main.tsx index 929d43c3..243d0b11 100644 --- a/ui/src/main.tsx +++ b/ui/src/main.tsx @@ -81,7 +81,7 @@ const router = createBrowserRouter([ element: , }, { - path: '/qc', + path: '/analyze', element: , }, ]); diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 02614b3b..bf1b06ad 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -1,26 +1,22 @@ import { useState, useRef } from 'react'; import { Layout } from '../components/layout.tsx'; -import { RegionSet, ChromosomeStats } from '@databio/gtars'; -import { handleBedFileInput, type BedEntry } from '../utils.ts'; +import { RegionSet } from '@databio/gtars'; +import { handleBedFileInput } from '../utils.ts'; +import { bytesToSize } from '../utils.ts'; import ChromosomeStatsPanel from '../components/bed-analytics-components/chromosome-stats-panel.tsx'; +import ChromosomeBarPlot from '../components/bed-analytics-components/bed-plots.tsx'; export const BEDAnalytics = () => { - const [regionsetRegions, setregionsetRegions] = useState(null); - const [Rs, setRs] = useState(null); + + const [rs, setRs] = useState(null); const [loadingRS, setLoadingRS] = useState(false); - const regionsetFileInputRef = useRef(null); const [totalProcessingTime, setTotalProcessingTime] = useState(null); const [selectedFile, setSelectedFile] = useState(null); const [inputMode, setInputMode] = useState<'file' | 'url'>('file'); const [bedUrl, setBedUrl] = useState(''); - const formatFileSize = (bytes: number): string => { - if (bytes === 0) return '0 B'; - const k = 1024; - const sizes = ['B', 'KB', 'MB', 'GB']; - const i = Math.floor(Math.log(bytes) / Math.log(k)); - return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i]; - }; + const regionsetFileInputRef = useRef(null); + const fetchBedFromUrl = async (url: string): Promise => { const response = await fetch(url); @@ -58,7 +54,6 @@ export const BEDAnalytics = () => { } as unknown as Event; await handleBedFileInput(syntheticEvent, (entries) => { - setregionsetRegions(entries); setTimeout(() => { const rs = new RegionSet(entries); @@ -78,9 +73,8 @@ export const BEDAnalytics = () => { } }; - const clearAll = () => { + const unloadFile = () => { setRs(null); - setregionsetRegions(null); setTotalProcessingTime(null); setSelectedFile(null); setBedUrl(''); @@ -133,7 +127,7 @@ export const BEDAnalytics = () => { onChange={(e) => { const file = e.target.files?.[0]; if (file) { - clearAll(); + unloadFile(); setSelectedFile(file); } }} @@ -141,7 +135,7 @@ export const BEDAnalytics = () => { {selectedFile && (
Selected file: {selectedFile.name}
-
File size: {formatFileSize(selectedFile.size)}
+
File size: {bytesToSize(selectedFile.size)}
)}
@@ -155,7 +149,7 @@ export const BEDAnalytics = () => { value={bedUrl} onChange={(e) => { setBedUrl(e.target.value); - if (Rs) clearAll(); + if (rs) unloadFile(); }} /> {bedUrl && ( @@ -166,7 +160,7 @@ export const BEDAnalytics = () => {
)} - {Rs && totalProcessingTime !== null && ( + {rs && totalProcessingTime !== null && (
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s
@@ -178,7 +172,7 @@ export const BEDAnalytics = () => { disabled={ (inputMode === 'file' && !selectedFile) || (inputMode === 'url' && !bedUrl.trim()) || - Rs !== null || + rs !== null || loadingRS } className="btn btn-primary" @@ -187,9 +181,9 @@ export const BEDAnalytics = () => { Analyze RegionSet @@ -208,7 +202,7 @@ export const BEDAnalytics = () => { )} - {Rs && !loadingRS && ( + {rs && !loadingRS && (
@@ -219,36 +213,53 @@ export const BEDAnalytics = () => { )}
- {Rs && ( + {rs && (
- + - + - + - +
Identifier{Rs.digest}{rs.digest}
Mean region width{Rs.mean_region_width}{rs.mean_region_width}
Total number of regions{Rs.total_nucleotides}{rs.total_nucleotides}
Total number of nucleotides{Rs.total_nucleotides}{rs.total_nucleotides}

Interval chromosome length statistics

- {Rs.calculate_statistics && ( - + {rs && ( + )}
+
+

Region Distribution Plot (DATA)

+ {rs && ( +
+ { + console.log('Chromosome bar clicked:', d); + }} + /> +
+ )} +
)}
From 5bdec960dd968e4af9db6dc3df51b23b42cf164a Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Fri, 24 Oct 2025 18:18:38 -0400 Subject: [PATCH 10/65] added region distribution plot --- .../bed-analytics-components/bed-plots.tsx | 25 +++++++++++-------- ui/src/pages/bed-analytics.tsx | 17 +++++++++---- 2 files changed, 26 insertions(+), 16 deletions(-) diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx index accb67ee..41f87426 100644 --- a/ui/src/components/bed-analytics-components/bed-plots.tsx +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -38,6 +38,9 @@ const distributionSpec = (data: any, props: Props = {}) => { strokeWidth: 0, cursor: 'inherit', }, + bar: { + continuousBandSize: 2.5, // This controls the bar width without spacing + }, }, data: { values: transformedData, @@ -51,17 +54,17 @@ const distributionSpec = (data: any, props: Props = {}) => { labelOrient: 'right', labelPadding: 5, }, - sort: [ - 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', - 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', - 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', - ], + // sort: [ + // 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', + // 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', + // 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', + // ], title: 'Number of Regions', type: 'ordinal', }, x: { axis: { - // labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'', + labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'', values: [0, 300.0], }, field: 'withinGroupID', @@ -73,7 +76,7 @@ const distributionSpec = (data: any, props: Props = {}) => { }, y: { axis: { - values: [10.0, 20.0, 30.0], + values: [10.0], }, field: 'N', title: '', @@ -82,15 +85,15 @@ const distributionSpec = (data: any, props: Props = {}) => { }, height: 25, mark: { - cornerRadiusEnd: 0.5, + cornerRadiusEnd: -0.5, type: 'bar', width: 2.5, }, - width: 750, + width: 'container', }; }; -export const ChromosomeBarPlot = (props: Props) => { +export const RegionDistributionPlot = (props: Props) => { const { data, xlab, ylab, height, color, action } = props; const plotRef = useRef(null); @@ -120,4 +123,4 @@ export const ChromosomeBarPlot = (props: Props) => { ); }; -export default ChromosomeBarPlot; +export default RegionDistributionPlot; diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index bf1b06ad..8838f8b7 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -4,7 +4,7 @@ import { RegionSet } from '@databio/gtars'; import { handleBedFileInput } from '../utils.ts'; import { bytesToSize } from '../utils.ts'; import ChromosomeStatsPanel from '../components/bed-analytics-components/chromosome-stats-panel.tsx'; -import ChromosomeBarPlot from '../components/bed-analytics-components/bed-plots.tsx'; +import RegionDistributionPlot from '../components/bed-analytics-components/bed-plots.tsx'; export const BEDAnalytics = () => { @@ -244,11 +244,18 @@ export const BEDAnalytics = () => { )}
-

Region Distribution Plot (DATA)

- {rs && ( + {/*

Region Distribution Plot (DATA)

*/} + {/*{rs && (*/} + {/*
*/} + {/* 
*/}
+                  {/*      {JSON.stringify(rs.calculate_region_distribution(), null, 2)}*/}
+                  {/*
*/} + {/*
*/} + {/*)}*/} + {rs && (
- Date: Fri, 24 Oct 2025 19:03:16 -0400 Subject: [PATCH 11/65] small adjustment for region distribution plot --- .../bed-analytics-components/bed-plots.tsx | 23 +++++++++++++++---- ui/src/pages/bed-analytics.tsx | 1 - 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx index 41f87426..44981474 100644 --- a/ui/src/components/bed-analytics-components/bed-plots.tsx +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -25,12 +25,25 @@ const distributionSpec = (data: any, props: Props = {}) => { return { $schema: 'https://vega-github.io/schema/vega-lite/v6.json', + title: { + text: 'Region Distribution Plot', + fontSize: 24, + fontWeight: 'bold', + anchor: 'middle', + offset: 10, + }, config: { axis: { grid: false, }, facet: { spacing: -1, + labelFontSize: 12, + titleFontSize: 12, + }, + header: { + labelFontSize: 12, + titleFontSize: 16, }, view: { continuousHeight: 300, @@ -54,11 +67,11 @@ const distributionSpec = (data: any, props: Props = {}) => { labelOrient: 'right', labelPadding: 5, }, - // sort: [ - // 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', - // 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', - // 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', - // ], + sort: [ + 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', + 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', + 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', + ], title: 'Number of Regions', type: 'ordinal', }, diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 8838f8b7..d3e18c43 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -244,7 +244,6 @@ export const BEDAnalytics = () => { )}
- {/*

Region Distribution Plot (DATA)

*/} {/*{rs && (*/} {/*
*/} {/* 
*/}

From 836221ba83fb8c7097239e542f4499437a6eac2c Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Fri, 24 Oct 2025 20:47:37 -0400
Subject: [PATCH 12/65] try random things

---
 ui/package-lock.json                          | 5381 ++++++++++++-----
 ui/package.json                               |    5 +-
 .../bed-splash-components/bed-atlas.tsx       |  221 +
 .../bed-splash-components/header.tsx          |    8 +-
 ui/src/components/nav/nav-desktop.tsx         |    8 +-
 ui/src/components/search/search-bar.tsx       |    2 +-
 ui/src/custom.scss                            |   25 +-
 ui/src/pages/bed-splash.tsx                   |    3 +
 ui/src/utils.ts                               |   23 +
 9 files changed, 4106 insertions(+), 1570 deletions(-)
 create mode 100644 ui/src/components/bed-splash-components/bed-atlas.tsx

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 8e03fbf4..b69667fb 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -18,6 +18,7 @@
         "chart.js": "^4.4.2",
         "chartjs-chart-error-bars": "^4.4.0",
         "chartjs-plugin-datalabels": "^2.2.0",
+        "embedding-atlas": "^0.11.0",
         "framer-motion": "^11.0.20",
         "js-yaml": "^4.1.0",
         "react": "^18.2.0",
@@ -50,48 +51,25 @@
         "vite": "^6.3.6"
       }
     },
-    "node_modules/@aashutoshrathi/word-wrap": {
-      "version": "1.2.6",
-      "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz",
-      "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==",
-      "dev": true,
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
-    "node_modules/@ampproject/remapping": {
-      "version": "2.3.0",
-      "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz",
-      "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==",
-      "dev": true,
-      "license": "Apache-2.0",
-      "dependencies": {
-        "@jridgewell/gen-mapping": "^0.3.5",
-        "@jridgewell/trace-mapping": "^0.3.24"
-      },
-      "engines": {
-        "node": ">=6.0.0"
-      }
-    },
     "node_modules/@babel/code-frame": {
-      "version": "7.26.2",
-      "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.26.2.tgz",
-      "integrity": "sha512-RJlIHRueQgwWitWgF8OdFYGZX328Ax5BCemNGlqHfplnRT9ESi8JkFlvaVYbS+UubVY6dpv87Fs2u5M29iNFVQ==",
+      "version": "7.27.1",
+      "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.27.1.tgz",
+      "integrity": "sha512-cjQ7ZlQ0Mv3b47hABuTevyTuYN4i+loJKGeV9flcCgIK37cCXRh+L1bd3iBHlynerhQ7BhCkn2BPbQUL+rGqFg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@babel/helper-validator-identifier": "^7.25.9",
+        "@babel/helper-validator-identifier": "^7.27.1",
         "js-tokens": "^4.0.0",
-        "picocolors": "^1.0.0"
+        "picocolors": "^1.1.1"
       },
       "engines": {
         "node": ">=6.9.0"
       }
     },
     "node_modules/@babel/compat-data": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.26.8.tgz",
-      "integrity": "sha512-oH5UPLMWR3L2wEFLnFJ1TZXqHufiTKAiLfqw5zkhS4dKXLJ10yVztfil/twG8EDTA4F/tvVNw9nOl4ZMslB8rQ==",
+      "version": "7.28.5",
+      "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.5.tgz",
+      "integrity": "sha512-6uFXyCayocRbqhZOB+6XcuZbkMNimwfVGFji8CTZnCzOHVGvDqzvitu1re2AU5LROliz7eQPhB8CpAMvnx9EjA==",
       "dev": true,
       "license": "MIT",
       "engines": {
@@ -99,22 +77,23 @@
       }
     },
     "node_modules/@babel/core": {
-      "version": "7.26.10",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.10.tgz",
-      "integrity": "sha512-vMqyb7XCDMPvJFFOaT9kxtiRh42GwlZEg1/uIgtZshS5a/8OaduUfCi7kynKgc3Tw/6Uo2D+db9qBttghhmxwQ==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@ampproject/remapping": "^2.2.0",
-        "@babel/code-frame": "^7.26.2",
-        "@babel/generator": "^7.26.10",
-        "@babel/helper-compilation-targets": "^7.26.5",
-        "@babel/helper-module-transforms": "^7.26.0",
-        "@babel/helpers": "^7.26.10",
-        "@babel/parser": "^7.26.10",
-        "@babel/template": "^7.26.9",
-        "@babel/traverse": "^7.26.10",
-        "@babel/types": "^7.26.10",
+      "version": "7.28.5",
+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.5.tgz",
+      "integrity": "sha512-e7jT4DxYvIDLk1ZHmU/m/mB19rex9sv0c2ftBtjSBv+kVM/902eh0fINUzD7UwLLNR+jU585GxUJ8/EBfAM5fw==",
+      "dev": true,
+      "license": "MIT",
+      "peer": true,
+      "dependencies": {
+        "@babel/code-frame": "^7.27.1",
+        "@babel/generator": "^7.28.5",
+        "@babel/helper-compilation-targets": "^7.27.2",
+        "@babel/helper-module-transforms": "^7.28.3",
+        "@babel/helpers": "^7.28.4",
+        "@babel/parser": "^7.28.5",
+        "@babel/template": "^7.27.2",
+        "@babel/traverse": "^7.28.5",
+        "@babel/types": "^7.28.5",
+        "@jridgewell/remapping": "^2.3.5",
         "convert-source-map": "^2.0.0",
         "debug": "^4.1.0",
         "gensync": "^1.0.0-beta.2",
@@ -140,16 +119,16 @@
       }
     },
     "node_modules/@babel/generator": {
-      "version": "7.27.0",
-      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.27.0.tgz",
-      "integrity": "sha512-VybsKvpiN1gU1sdMZIp7FcqphVVKEwcuj02x73uvcHE0PTihx1nlBcowYWhDwjpoAXRv43+gDzyggGnn1XZhVw==",
+      "version": "7.28.5",
+      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.5.tgz",
+      "integrity": "sha512-3EwLFhZ38J4VyIP6WNtt2kUdW9dokXA9Cr4IVIFHuCpZ3H8/YFOl5JjZHisrn1fATPBmKKqXzDFvh9fUwHz6CQ==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
-        "@babel/parser": "^7.27.0",
-        "@babel/types": "^7.27.0",
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-      "integrity": "sha512-d2JWLCivmZYTSIoge9MsgFCZrt571BikcWGYkjC1khllbTeDlGqZ2D8vD8E/lJa8WGWbb7Plm8/XJYV7IJHZZw==",
-      "peer": true,
-      "engines": {
-        "node": ">= 8"
-      }
-    },
     "node_modules/which": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
       "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
-      "dev": true,
+      "license": "ISC",
       "dependencies": {
         "isexe": "^2.0.0"
       },
@@ -5910,11 +8107,30 @@
         "node": ">= 8"
       }
     },
+    "node_modules/word-wrap": {
+      "version": "1.2.5",
+      "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.5.tgz",
+      "integrity": "sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/wordwrapjs": {
+      "version": "5.1.1",
+      "resolved": "https://registry.npmjs.org/wordwrapjs/-/wordwrapjs-5.1.1.tgz",
+      "integrity": "sha512-0yweIbkINJodk27gX9LBGMzyQdBDan3s/dEAiwBOj+Mf0PPyWL6/rikalkv8EeD0E8jm4o5RXEOrFTP3NXbhJg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12.17"
+      }
+    },
     "node_modules/wrap-ansi": {
-      "version": "9.0.0",
-      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.0.tgz",
-      "integrity": "sha512-G8ura3S+3Z2G+mkgNRq8dqaFZAuxfsxpBB8OCTGRTCtp+l/v9nbFNmCUP1BZMts3G1142MsZfn6eeUKrr4PD1Q==",
-      "peer": true,
+      "version": "9.0.2",
+      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.2.tgz",
+      "integrity": "sha512-42AtmgqjV+X1VpdOfyTGOYRi0/zsoLqtXQckTmqTeybT+BDIbM/Guxo7x3pE2vtpr1ok6xRqM9OpBe+Jyoqyww==",
+      "license": "MIT",
       "dependencies": {
         "ansi-styles": "^6.2.1",
         "string-width": "^7.0.0",
@@ -5927,11 +8143,49 @@
         "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
       }
     },
+    "node_modules/wrap-ansi-cjs": {
+      "name": "wrap-ansi",
+      "version": "7.0.0",
+      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
+      "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
+      "license": "MIT",
+      "dependencies": {
+        "ansi-styles": "^4.0.0",
+        "string-width": "^4.1.0",
+        "strip-ansi": "^6.0.0"
+      },
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
+      }
+    },
+    "node_modules/wrap-ansi-cjs/node_modules/emoji-regex": {
+      "version": "8.0.0",
+      "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
+      "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==",
+      "license": "MIT"
+    },
+    "node_modules/wrap-ansi-cjs/node_modules/string-width": {
+      "version": "4.2.3",
+      "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
+      "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==",
+      "license": "MIT",
+      "dependencies": {
+        "emoji-regex": "^8.0.0",
+        "is-fullwidth-code-point": "^3.0.0",
+        "strip-ansi": "^6.0.1"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/wrap-ansi/node_modules/ansi-regex": {
-      "version": "6.1.0",
-      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.1.0.tgz",
-      "integrity": "sha512-7HSX4QQb4CspciLpVFwyRe79O3xsIZDDLER21kERQ71oaPodF8jL725AgJMFAYbooIqolJoRLuM81SpeUkpkvA==",
-      "peer": true,
+      "version": "6.2.2",
+      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.2.2.tgz",
+      "integrity": "sha512-Bq3SmSpyFHaWjPk8If9yc6svM8c56dB5BAtW4Qbw5jHTwwXXcTLoRMkpDJp6VL0XzlWaCHTXrkFURMYmD0sLqg==",
+      "license": "MIT",
       "engines": {
         "node": ">=12"
       },
@@ -5939,11 +8193,23 @@
         "url": "https://github.com/chalk/ansi-regex?sponsor=1"
       }
     },
+    "node_modules/wrap-ansi/node_modules/ansi-styles": {
+      "version": "6.2.3",
+      "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.3.tgz",
+      "integrity": "sha512-4Dj6M28JB+oAH8kFkTLUo+a2jwOFkuqb3yucU0CANcRRUbxS0cP0nZYCGjcc3BNXwRIsUVmDGgzawme7zvJHvg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/ansi-styles?sponsor=1"
+      }
+    },
     "node_modules/wrap-ansi/node_modules/strip-ansi": {
-      "version": "7.1.0",
-      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz",
-      "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==",
-      "peer": true,
+      "version": "7.1.2",
+      "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.2.tgz",
+      "integrity": "sha512-gmBGslpoQJtgnMAvOVqGZpEz9dyoKTCzy2nfz/n8aIFhN/jCE/rCmcxabB6jOOHV+0WNnylOxaxBQPSvcWklhA==",
+      "license": "MIT",
       "dependencies": {
         "ansi-regex": "^6.0.1"
       },
@@ -5958,13 +8224,14 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
       "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==",
-      "dev": true
+      "dev": true,
+      "license": "ISC"
     },
     "node_modules/y18n": {
       "version": "5.0.8",
       "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz",
       "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==",
-      "peer": true,
+      "license": "ISC",
       "engines": {
         "node": ">=10"
       }
@@ -5980,7 +8247,7 @@
       "version": "18.0.0",
       "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.0.0.tgz",
       "integrity": "sha512-4UEqdc2RYGHZc7Doyqkrqiln3p9X2DZVxaGbwhn2pi7MrRagKaOcIKe8L3OxYcbhXLgLFUS3zAYuQjKBQgmuNg==",
-      "peer": true,
+      "license": "MIT",
       "dependencies": {
         "cliui": "^9.0.1",
         "escalade": "^3.1.1",
@@ -5997,7 +8264,7 @@
       "version": "22.0.0",
       "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-22.0.0.tgz",
       "integrity": "sha512-rwu/ClNdSMpkSrUb+d6BRsSkLUq1fmfsY6TOpYzTwvwkg1/NRG85KBy3kq++A8LKQwX6lsu+aWad+2khvuXrqw==",
-      "peer": true,
+      "license": "ISC",
       "engines": {
         "node": "^20.19.0 || ^22.12.0 || >=23"
       }
@@ -6007,6 +8274,7 @@
       "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
       "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
       "dev": true,
+      "license": "MIT",
       "engines": {
         "node": ">=10"
       },
@@ -6018,6 +8286,7 @@
       "version": "2.0.4",
       "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
       "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
+      "license": "MIT",
       "funding": {
         "type": "github",
         "url": "https://github.com/sponsors/wooorm"
diff --git a/ui/package.json b/ui/package.json
index 081c74b0..a6a7caac 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -22,6 +22,7 @@
     "chart.js": "^4.4.2",
     "chartjs-chart-error-bars": "^4.4.0",
     "chartjs-plugin-datalabels": "^2.2.0",
+    "embedding-atlas": "^0.11.0",
     "framer-motion": "^11.0.20",
     "js-yaml": "^4.1.0",
     "react": "^18.2.0",
@@ -35,8 +36,8 @@
     "react-markdown": "^9.0.1",
     "react-router-dom": "^7.5.2",
     "rehype-highlight": "^7.0.0",
-    "vega-embed": "^7.0.2",
-    "three": "^0.177.0"
+    "three": "^0.177.0",
+    "vega-embed": "^7.0.2"
   },
   "devDependencies": {
     "@types/js-yaml": "^4.0.9",
diff --git a/ui/src/components/bed-splash-components/bed-atlas.tsx b/ui/src/components/bed-splash-components/bed-atlas.tsx
new file mode 100644
index 00000000..d7257694
--- /dev/null
+++ b/ui/src/components/bed-splash-components/bed-atlas.tsx
@@ -0,0 +1,221 @@
+import { EmbeddingAtlas } from 'embedding-atlas/react';
+import { useEffect, useState, useRef, useMemo } from 'react';
+import * as vg from '@uwdata/vgplot'
+import { tableau20 } from '../../utils';
+
+type Props = {
+  bedId: string;
+  neighbors?: any;
+}
+
+export const BEDAtlas = (props: Props) => {
+  const {  } = props;
+
+  const dotPlotRef = useRef(null);
+  const colorLegendRef = useRef(null);
+  const containerRef = useRef(null);
+
+  const [containerWidth, setContainerWidth] = useState(900);
+  const [isReady, setIsReady] = useState(false);
+  const [colorGrouping, setColorGrouping] = useState('cell_line');
+
+  const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []);
+  const $legendSelection = vg.Selection.intersect();
+
+  const initializeData = async (coordinator: any) => {
+    const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json';
+    await coordinator.exec([
+      vg.sql`CREATE OR REPLACE TABLE data AS 
+            SELECT 
+              unnest(nodes, recursive := true)
+            FROM read_json_auto('${url}')`,
+      // vg.sql`CREATE OR REPLACE TABLE data AS
+      //       SELECT 
+      //         *,
+      //         (DENSE_RANK() OVER (ORDER BY assay) - 1)::INTEGER AS assay_category,
+      //         (DENSE_RANK() OVER (ORDER BY cell_line) - 1)::INTEGER AS cell_line_category
+      //       FROM data`
+    ]);
+  }
+
+  const plotData = () => {
+    let bedQuery = vg.Query.from('data')
+      .select(
+        'x',
+        'y',
+        'id',
+        'name',
+        'description',
+        'assay',
+        'cell_line',
+      );
+
+    const dotPlot = vg.plot(
+        vg.dot(vg.from(bedQuery, {}), {
+          x: 'x',
+          y: 'y',
+          z: colorGrouping,
+          fill: colorGrouping,
+          colorRange: tableau20,
+          opacity: 0.5,
+          r: 1.5,
+          channels: { 'Name:': 'name', 'Cell Line:': 'cell_line', 'Assay:': 'assay' },
+          tip: {
+            format: {
+              'Name:': true,
+              'Cell Line:': true,
+              'Assay:': true,
+              x: false,
+              y: false,
+              z: false,
+              fill: false
+            },
+          },
+        }),
+        vg.highlight({ by: $legendSelection, fill: '#ccc', fillOpacity: 0.2 }),
+        vg.region({ as: $legendSelection, channels: ['z'] }),
+        vg.name('dotPlot'),
+        vg.width(containerWidth),
+        vg.height(500),
+        vg.xLabel(null),
+        vg.yLabel(null),
+        // vg.gridY(),
+        // vg.gridX(),
+      );
+
+    const colorLegend = vg.colorLegend({
+      for: 'dotPlot',
+      as: $legendSelection,
+      columns: 1,
+    });
+
+    if (dotPlotRef.current) dotPlotRef.current.replaceChildren(dotPlot);
+    if (colorLegendRef.current) colorLegendRef.current.replaceChildren(colorLegend);
+  }
+
+  useEffect(() => {
+    vg.coordinator(coordinator);
+
+    if (containerRef.current) {
+      setContainerWidth(containerRef.current.offsetWidth);
+    }
+    plotData()
+  }, [isReady, colorGrouping]);
+
+  useEffect(() => {
+    initializeData(coordinator).then(() => setIsReady(true));
+  }, []);
+
+  return (
+    <>
+      {isReady && (
+        <>
+        

+          
Embedding Atlas

+          

+            

+              

+                {/*  */}
+                

+              

+            

+          

+          

+            

+              

+                Legend
+                

+                   setColorGrouping(e.target.value)}
+                  />
+                  
+                   setColorGrouping(e.target.value)}
+                  />
+                  
+                

+              

+              

+                

+              

+            

+
+            

+              

+                {/* {selectedPoint ? (
+                  

+                    
Name: {selectedPoint.name}

+                    
Cell Line: {selectedPoint.cell_line}

+                    
Assay: {selectedPoint.assay}

+                    
Description: {selectedPoint.description}

+                  

+                ) : (
+                  
Click a point to view details.

+                )} */}
+              

+            

+          

+        

+        

+          

+            

+              

+                

+                  
+                

+              

+            

+          

+        

+        
+      )}
+    
+  );
+}
\ No newline at end of file
diff --git a/ui/src/components/bed-splash-components/header.tsx b/ui/src/components/bed-splash-components/header.tsx
index 5bf6c884..3fe26a19 100644
--- a/ui/src/components/bed-splash-components/header.tsx
+++ b/ui/src/components/bed-splash-components/header.tsx
@@ -152,12 +152,12 @@ export const BedSplashHeader = (props: Props) => {
                 
                   {metadata.files?.bed_file && (
                     
-                      {(metadata.files?.bed_file?.access_methods || []).map((method) => {
+                      {(metadata.files?.bed_file?.access_methods || []).map((method, index) => {
                         if (method.type === 'local' || method.type === 's3') {
                           return null;
                         }
                         return (
-                          
+                          
                             {method.access_id ? 'BED file' : 'No download link available'} (
                             {bytesToSize(metadata.files?.bed_file?.size || 0)})
                           
@@ -167,12 +167,12 @@ export const BedSplashHeader = (props: Props) => {
                   )}
                   {metadata.files?.bigbed_file && (
                     
-                      {(metadata.files?.bigbed_file?.access_methods || []).map((method) => {
+                      {(metadata.files?.bigbed_file?.access_methods || []).map((method, index) => {
                         if (method.type === 'local' || method.type === 's3') {
                           return null;
                         }
                         return (
-                          
+                          
                             {method.access_id ? 'BigBED file' : 'No download link available'} (
                             {bytesToSize(metadata.files?.bigbed_file?.size || 0)})
                           
diff --git a/ui/src/components/nav/nav-desktop.tsx b/ui/src/components/nav/nav-desktop.tsx
index 61b12094..1b4cf09a 100644
--- a/ui/src/components/nav/nav-desktop.tsx
+++ b/ui/src/components/nav/nav-desktop.tsx
@@ -6,22 +6,22 @@ export const NavDesktop = () => {
   const { cart } = useBedCart();
   return (
       
    
-          
  • 
+          
  • 
               
                   GitHub
               
           
    • 
-          
  • 
+          
  • 
               
                   Docs
               
           
    • 
-          
  • 
+          
  • 
               
                   API
               
           
    • 
-          
  • 
+          
  • 
               
                   Search
               
diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/search-bar.tsx
index 2538b429..e1437aa1 100644
--- a/ui/src/components/search/search-bar.tsx
+++ b/ui/src/components/search/search-bar.tsx
@@ -74,7 +74,7 @@ export const SearchBar = (props: Props) => {
         
         {searchView === 't2b' && (
           

             

 
-            

-              

-                {/* {selectedPoint ? (
-                  

-                    
Name: {selectedPoint.name}

-                    
Cell Line: {selectedPoint.cell_line}

-                    
Assay: {selectedPoint.assay}

-                    
Description: {selectedPoint.description}

-                  

-                ) : (
-                  
Click a point to view details.

-                )} */}
+            

+              

+                Selected Points
+                
+              

+              

+                
+                  
+                    
+                      
+                      
+                      
+                      
+                    
+                  
+                  
+                    {selectedPoints?.map((point: any, index: number) => (
+                       centerOnPoint(point, 0.3)} key={index}>
+                        
+                        
+                        
+                        
+                      
+                    ))}
+                  
+                
BED NameAssayCell LineDescription
{point.text}{point.fields.Assay}{point.fields['Cell Line']}{point.fields.Description}

               

             

           

diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx
index e2c67436..42ce9fb3 100644
--- a/ui/src/pages/bed-splash.tsx
+++ b/ui/src/pages/bed-splash.tsx
@@ -17,7 +17,7 @@ import { snakeToTitleCase } from '../utils';
 import { Text2BedSearchResultsTable } from '../components/search/text2bed/t2b-search-results-table';
 import { useBedNeighbours } from '../queries/useBedNeighbours';
 import type { components } from '../../bedbase-types.d.ts';
-import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx';
+// import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx';
 import { BADAtlas } from '../components/bed-splash-components/bad-atlas.tsx';
 
 // Use the response type to properly type the metadata
@@ -272,7 +272,7 @@ export const BedSplash = () => {
             
           
 
-          {bedId && (
+          {bedId && metadata?.name?.includes('encode') && (
             <>
               
               {/*  */}
diff --git a/ui/src/utils.ts b/ui/src/utils.ts
index c1721082..dcc06875 100644
--- a/ui/src/utils.ts
+++ b/ui/src/utils.ts
@@ -165,4 +165,18 @@ export const tableau20 = [
     '#dbdb8d',
     '#17becf',
     '#9edae5',
-  ];
\ No newline at end of file
+  ];
+
+// Point-in-polygon test using ray casting algorithm
+export const isPointInPolygon = (point: {x: number, y: number}, polygon: {x: number, y: number}[]) => {
+  let inside = false;
+  for (let i = 0, j = polygon.length - 1; i < polygon.length; j = i++) {
+    const xi = polygon[i].x, yi = polygon[i].y;
+    const xj = polygon[j].x, yj = polygon[j].y;
+
+    const intersect = ((yi > point.y) !== (yj > point.y))
+        && (point.x < (xj - xi) * (point.y - yi) / (yj - yi) + xi);
+    if (intersect) inside = !inside;
+  }
+  return inside;
+};
\ No newline at end of file

From 1d12aa3914942de4e1bd1d30decdb369679e6a0e Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Wed, 29 Oct 2025 20:07:20 -0400
Subject: [PATCH 22/65] neighbors in atlas

---
 .../bed-splash-components/bad-atlas.tsx       | 129 ++++++++++++++----
 ui/src/pages/bed-splash.tsx                   |  24 +++-
 2 files changed, 121 insertions(+), 32 deletions(-)

diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx
index 44df6520..8e0d5446 100644
--- a/ui/src/components/bed-splash-components/bad-atlas.tsx
+++ b/ui/src/components/bed-splash-components/bad-atlas.tsx
@@ -4,16 +4,20 @@ import * as vg from '@uwdata/vgplot'
 
 import { isPointInPolygon, tableau20 } from '../../utils';
 import { useBedCart } from '../../contexts/bedcart-context';
+import { components } from '../../../bedbase-types';
+
+type SearchResponse = components['schemas']['BedListSearchResult'];
 
 type Props = {
   bedId: string;
-  neighbors?: any;
+  neighbors?: SearchResponse;
+  showNeighbors?: boolean;
 }
 
 export const BADAtlas = (props: Props) => {
-  const { bedId } = props;
+  const { bedId, neighbors, showNeighbors } = props;
   const { addBedToCart } = useBedCart();
-  
+
   const containerRef = useRef(null);
 
   const [containerWidth, setContainerWidth] = useState(900);
@@ -25,13 +29,15 @@ export const BADAtlas = (props: Props) => {
   const [legendItems, setLegendItems] = useState([]);
   const [filterSelection, setFilterSelection] = useState(null);
   const [addedToCart, setAddedToCart] = useState(false);
+  const [tooltipPoint, setTooltipPoint] = useState(null);
 
   const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []);
   const filter = useMemo(() => vg.Selection.intersect(), []);
-  // Create a stable source object for legend filter updates
   const legendFilterSource = useMemo(() => ({}), []);
+  const neighborIDs = useMemo(() => neighbors?.results?.map(result => result.id), [neighbors]);
 
   const centerOnPoint = (point: any, scale: number = 1) => {
+    setTooltipPoint(point);
     setViewportState({
       x: point.x,
       y: point.y,
@@ -39,18 +45,34 @@ export const BADAtlas = (props: Props) => {
     });
   };
 
+  const getSortedSelectedPoints = () => {
+    if (!selectedPoints || selectedPoints.length === 0) return [];
+
+    const currentBed = selectedPoints.find((p: any) => p.identifier === bedId);
+    const others = selectedPoints.filter((p: any) => p.identifier !== bedId);
+
+    if (neighbors?.results && neighbors.results.length > 0) {
+      const scoreMap = new Map(neighbors.results.map(n => [n.id, n.score]));
+      others.sort((a: any, b: any) => {
+        const scoreA = scoreMap.get(a.identifier) || 0;
+        const scoreB = scoreMap.get(b.identifier) || 0;
+        return scoreB - scoreA; // Descending order
+      });
+    }
+
+    return currentBed ? [currentBed, ...others] : others;
+  };
+
   const handleLegendClick = (item: any) => {
     if (filterSelection?.category === item.category) {
       setFilterSelection(null);
-      // Clear the filter by updating with null predicate using the same source
       filter.update({
-        source: legendFilterSource,
+        source: legendFilterSource, // memoized so that mosaic can keep track of source and clear previous selection
         value: null,
         predicate: null
       });
     } else {
       setFilterSelection(item);
-      // Update with new filter - will replace previous clause from same source
       filter.update({
         source: legendFilterSource,
         value: item.category,
@@ -62,17 +84,32 @@ export const BADAtlas = (props: Props) => {
   const handlePointSelection = (dataPoints: any[] | null) => {
     // console.log('Selection changed via onSelection callback:', dataPoints);
     const points = dataPoints || [];
+    const hasInitialPoint = points.some(p => p.identifier === initialPoint?.identifier);
+    let finalPoints = hasInitialPoint ? points : (initialPoint ? [initialPoint, ...points] : points);
 
-    if (initialPoint) {
-      const hasInitialPoint = points.some(p => p.identifier === initialPoint.identifier);
-      if (!hasInitialPoint) {
-        setSelectedPoints([initialPoint, ...points]);
-      } else {
-        setSelectedPoints(points);
+    if (showNeighbors && neighborIDs && neighborIDs.length > 0) {
+      const selectedIds = new Set(finalPoints.map((p: any) => p.identifier));
+      const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id));
+
+      if (missingNeighborIds.length > 0) {
+        coordinator.query(
+          `SELECT
+            x, y,
+            ${colorGrouping} as category,
+            name as text,
+            id as identifier,
+            {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
+           FROM data
+           WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`,
+          { type: 'json' }
+        ).then((neighborPoints: any) => {
+          setSelectedPoints([...finalPoints, ...neighborPoints]);
+        });
+        return;
       }
-    } else {
-      setSelectedPoints(points);
     }
+
+    setSelectedPoints(finalPoints);
   };
 
   // Range selection (for rectangle/lasso)
@@ -140,16 +177,31 @@ export const BADAtlas = (props: Props) => {
     }
 
     if (result && result.length > 0) {
-      if (initialPoint) {
-        const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint.identifier);
-        if (!hasInitialPoint) {
-          setSelectedPoints([initialPoint, ...result]);
-        } else {
-          setSelectedPoints(result);
+      // Always ensure initialPoint is included
+      const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint?.identifier);
+      let finalPoints = hasInitialPoint ? result : (initialPoint ? [initialPoint, ...result] : result);
+
+      if (showNeighbors && neighborIDs && neighborIDs.length > 0) {
+        const selectedIds = new Set(finalPoints.map((p: any) => p.identifier));
+        const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id));
+
+        if (missingNeighborIds.length > 0) { // fetch missing neighbor points
+          const neighborPoints = await coordinator.query(
+            `SELECT
+              x, y,
+              ${colorGrouping} as category,
+              name as text,
+              id as identifier,
+              {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
+             FROM data
+             WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`,
+            { type: 'json' }
+          ) as any[];
+          finalPoints = [...finalPoints, ...neighborPoints];
         }
-      } else {
-        setSelectedPoints(result);
       }
+
+      setSelectedPoints(finalPoints);
     }
   };
 
@@ -202,10 +254,10 @@ export const BADAtlas = (props: Props) => {
     }
   }, [isReady, colorGrouping])
 
-  useEffect(() => { // fetch initial bed id
+  useEffect(() => { // fetch initial bed id and neighbors
     if (isReady) {
       setTimeout(async () => {
-        const points: any = await coordinator.query(
+        const currentBed: any = await coordinator.query(
           `SELECT
             x, y,
             ${colorGrouping} as category,
@@ -216,14 +268,29 @@ export const BADAtlas = (props: Props) => {
            WHERE id = '${bedId}'`,
           { type: 'json' }
         );
+        if (!currentBed || currentBed.length === 0) return;
+        setInitialPoint(currentBed[0]);
+        setTooltipPoint(currentBed[0]);
 
-        if (points && points.length > 0) {
-          setInitialPoint(points[0]);
-          setSelectedPoints([points[0]]);
+        if (showNeighbors && neighborIDs && neighborIDs.length > 0) {
+          const neighborPoints: any = await coordinator.query(
+            `SELECT
+              x, y,
+              ${colorGrouping} as category,
+              name as text,
+              id as identifier,
+              {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
+             FROM data
+             WHERE id IN (${neighborIDs.map(id => `'${id}'`).join(',')})`,
+            { type: 'json' }
+          );
+          setSelectedPoints([currentBed[0], ...neighborPoints]);
+        } else {
+          setSelectedPoints([currentBed[0]]);
         }
       }, 200);
     }
-  }, [isReady, bedId, coordinator, colorGrouping]);
+  }, [isReady, bedId, coordinator, colorGrouping, showNeighbors, neighborIDs]);
 
 
   return (
@@ -237,6 +304,7 @@ export const BADAtlas = (props: Props) => {
             

               

                  {
                   filter={filter}
                   viewportState={viewportState}
                   onViewportState={setViewportState}
+                  tooltip={tooltipPoint}
                   selection={selectedPoints}
                   onSelection={handlePointSelection}
                   onRangeSelection={(e) => handleRangeSelection(coordinator, e)}
@@ -358,7 +427,7 @@ export const BADAtlas = (props: Props) => {
                     
                   
                   
-                    {selectedPoints?.map((point: any, index: number) => (
+                    {getSortedSelectedPoints().map((point: any, index: number) => (
                        centerOnPoint(point, 0.3)} key={index}>
                         {point.text}
                         {point.fields.Assay}
diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx
index 42ce9fb3..8b2857ee 100644
--- a/ui/src/pages/bed-splash.tsx
+++ b/ui/src/pages/bed-splash.tsx
@@ -19,6 +19,7 @@ import { useBedNeighbours } from '../queries/useBedNeighbours';
 import type { components } from '../../bedbase-types.d.ts';
 // import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx';
 import { BADAtlas } from '../components/bed-splash-components/bad-atlas.tsx';
+import { useState } from 'react';
 
 // Use the response type to properly type the metadata
 type BedMetadata = components['schemas']['BedMetadataAll'];
@@ -27,6 +28,8 @@ export const BedSplash = () => {
   const params = useParams();
   const bedId = params.id;
 
+  const [showNeighbors, setShowNeighbors] = useState(true);
+
   const {
     isLoading,
     data: metadata,
@@ -274,14 +277,31 @@ export const BedSplash = () => {
 
           {bedId && metadata?.name?.includes('encode') && (
             <>
-              
+              
               {/*  */}
             
           )}
 
           {neighbours && (
             
-              
Similar BED Files

+              

+                
Similar BED Files

+                

+                   setShowNeighbors(!showNeighbors)}
+                  />
+                  
+                

+              

               
                 
               

From f28ae299839805998144d97af3e720c749e55bd4 Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Thu, 30 Oct 2025 15:43:26 -0400
Subject: [PATCH 23/65] ui updates and mosaic coordinator context

---
 .../bed-splash-components/atlas-tooltip.tsx   | 70 +++++++++++++++++
 .../bed-splash-components/bad-atlas.tsx       | 75 ++++++++++---------
 .../bed-atlas.tsx                             | 33 ++++----
 ui/src/components/search/search-selector.tsx  | 12 ++-
 .../contexts/mosaic-coordinator-context.tsx   | 64 ++++++++++++++++
 ui/src/main.tsx                               |  7 +-
 ui/src/pages/bed-splash.tsx                   |  2 +-
 ui/src/pages/search.tsx                       |  5 +-
 8 files changed, 209 insertions(+), 59 deletions(-)
 create mode 100644 ui/src/components/bed-splash-components/atlas-tooltip.tsx
 rename ui/src/components/{bed-splash-components => search}/bed-atlas.tsx (53%)
 create mode 100644 ui/src/contexts/mosaic-coordinator-context.tsx

diff --git a/ui/src/components/bed-splash-components/atlas-tooltip.tsx b/ui/src/components/bed-splash-components/atlas-tooltip.tsx
new file mode 100644
index 00000000..a9168114
--- /dev/null
+++ b/ui/src/components/bed-splash-components/atlas-tooltip.tsx
@@ -0,0 +1,70 @@
+import { createRoot, Root } from 'react-dom/client';
+
+interface TooltipProps {
+  tooltip?: {
+    text: string;
+    identifier: string;
+    fields?: {
+      Assay: string;
+      'Cell Line': string;
+      Description: string;
+    };
+    category?: string;
+  };
+}
+
+const TooltipContent = ({ tooltip }: { tooltip: TooltipProps['tooltip'] }) => {
+  if (!tooltip) return null;
+
+  return (
+    

+      
{tooltip.text || 'Unnamed BED'}

+      {tooltip.fields && (
+        <>
+          

+            {tooltip.fields.Description || 'No description available'}
+          

+          

+            
+              cell_line:{' '}{tooltip.fields['Cell Line'] || 'N/A'}
+            
+            
+              assay:{' '}{tooltip.fields.Assay || 'N/A'}
+            
+            
+              id:{' '}{tooltip.identifier || 'N/A'}
+            
+          

+        
+      )}
+    

+  );
+};
+
+export class AtlasTooltip {
+  private root: Root;
+
+  constructor(target: HTMLElement, props: TooltipProps) {
+    // Create a React root and render your component
+    this.root = createRoot(target);
+    this.update(props);
+  }
+
+  update(props: TooltipProps) {
+    // Re-render with new props
+    this.root.render();
+  }
+
+  destroy() {
+    // Unmount the React component
+    this.root.unmount();
+  }
+}
\ No newline at end of file
diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx
index 8e0d5446..bcbe8676 100644
--- a/ui/src/components/bed-splash-components/bad-atlas.tsx
+++ b/ui/src/components/bed-splash-components/bad-atlas.tsx
@@ -5,6 +5,8 @@ import * as vg from '@uwdata/vgplot'
 import { isPointInPolygon, tableau20 } from '../../utils';
 import { useBedCart } from '../../contexts/bedcart-context';
 import { components } from '../../../bedbase-types';
+import { AtlasTooltip } from './atlas-tooltip';
+import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
 
 type SearchResponse = components['schemas']['BedListSearchResult'];
 
@@ -16,6 +18,7 @@ type Props = {
 
 export const BADAtlas = (props: Props) => {
   const { bedId, neighbors, showNeighbors } = props;
+  const { coordinator, initializeData } = useMosaicCoordinator();
   const { addBedToCart } = useBedCart();
 
   const containerRef = useRef(null);
@@ -31,7 +34,6 @@ export const BADAtlas = (props: Props) => {
   const [addedToCart, setAddedToCart] = useState(false);
   const [tooltipPoint, setTooltipPoint] = useState(null);
 
-  const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []);
   const filter = useMemo(() => vg.Selection.intersect(), []);
   const legendFilterSource = useMemo(() => ({}), []);
   const neighborIDs = useMemo(() => neighbors?.results?.map(result => result.id), [neighbors]);
@@ -109,6 +111,7 @@ export const BADAtlas = (props: Props) => {
       }
     }
 
+    // setTooltipPoint(finalPoints.slice(-1)[0])
     setSelectedPoints(finalPoints);
   };
 
@@ -205,22 +208,6 @@ export const BADAtlas = (props: Props) => {
     }
   };
 
-  const initializeData = async (coordinator: any) => {
-    const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json';
-    await coordinator.exec([
-      vg.sql`CREATE OR REPLACE TABLE data AS
-            SELECT
-              unnest(nodes, recursive := true)
-            FROM read_json_auto('${url}')`,
-      vg.sql`CREATE OR REPLACE TABLE data AS
-            SELECT
-              *,
-              (DENSE_RANK() OVER (ORDER BY assay) - 1)::INTEGER AS assay_category,
-              (DENSE_RANK() OVER (ORDER BY cell_line) - 1)::INTEGER AS cell_line_category
-            FROM data`
-    ]);
-  }
-
   const fetchLegendItems = async (coordinator: any) => {
     const result = await coordinator.query(
       `SELECT DISTINCT
@@ -235,7 +222,7 @@ export const BADAtlas = (props: Props) => {
   }
 
   useEffect(() => { // initialize data
-    initializeData(coordinator).then(() => {
+    initializeData().then(() => {
       setIsReady(true);
     });
   }, []);
@@ -292,19 +279,19 @@ export const BADAtlas = (props: Props) => {
     }
   }, [isReady, bedId, coordinator, colorGrouping, showNeighbors, neighborIDs]);
 
-
   return (
     <>
-      {isReady && (
-      

-          

-            
BED Embedding Atlas

-          

-          

+      

+        

+          
BED Embedding Atlas

+        

+      

+      {isReady ? (
+        

+          

             

               

                  {
                   viewportState={viewportState}
                   onViewportState={setViewportState}
                   tooltip={tooltipPoint}
+                  customTooltip={{
+                    class: AtlasTooltip,
+                    props: {}
+                  }}
                   selection={selectedPoints}
                   onSelection={handlePointSelection}
                   onRangeSelection={(e) => handleRangeSelection(coordinator, e)}
@@ -330,8 +321,8 @@ export const BADAtlas = (props: Props) => {
               

             

           

-          

-            

+          

+            

               

                 Legend
                 

@@ -378,9 +369,16 @@ export const BADAtlas = (props: Props) => {
                         onClick={() => handleLegendClick(item)}
                         key={item.category}
                       >
-                        
-                          
-                          {item.name}
+                        
+                          
+                            
+                            {item.name}
+                          
+                          {(filterSelection?.category === item.category) && (
+                            
+                          )}
                         
                       
                     ))}
@@ -389,11 +387,12 @@ export const BADAtlas = (props: Props) => {
               

             

 
-            

+            

               

-                Selected Points
+                Selection
+                {/*  */}
                 
+                {/*  */}
               

               

                 
@@ -441,6 +442,12 @@ export const BADAtlas = (props: Props) => {
             
+      ) : (
+        

+          

+            Loading...
+          

+        

       )}
     
   );
diff --git a/ui/src/components/bed-splash-components/bed-atlas.tsx b/ui/src/components/search/bed-atlas.tsx
similarity index 53%
rename from ui/src/components/bed-splash-components/bed-atlas.tsx
rename to ui/src/components/search/bed-atlas.tsx
index 0c6ce962..d7799159 100644
--- a/ui/src/components/bed-splash-components/bed-atlas.tsx
+++ b/ui/src/components/search/bed-atlas.tsx
@@ -1,7 +1,6 @@
 import { EmbeddingAtlas } from 'embedding-atlas/react';
-import { useEffect, useState, useMemo } from 'react';
-import * as vg from '@uwdata/vgplot'
-
+import { useEffect, useState } from 'react';
+import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
 type Props = {
   bedId?: string;
   neighbors?: any;
@@ -11,38 +10,26 @@ export const BEDAtlas = (props: Props) => {
   const {} = props;
 
   const [isReady, setIsReady] = useState(false);
-
-  const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []);
-  const initializeData = async (coordinator: any) => {
-    const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json';
-    await coordinator.exec([
-      vg.sql`CREATE OR REPLACE TABLE data AS 
-            SELECT 
-              unnest(nodes, recursive := true)
-            FROM read_json_auto('${url}')`
-    ]);
-  }
+  const { coordinator, initializeData } = useMosaicCoordinator();
 
   useEffect(() => {
-    initializeData(coordinator).then(() => setIsReady(true));
+    initializeData().then(() => setIsReady(true));
   }, []);
 
   return (
     <>
-      {isReady && (
+      {isReady ? (
         

           

-            

-              Embedding Atlas
-            

             

-              

+              

                  {
             

           

         

+      ) : (
+        

+          

+            Loading...
+          

+        

       )}
     
   );
diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx
index 41cef61c..94ffa07f 100644
--- a/ui/src/components/search/search-selector.tsx
+++ b/ui/src/components/search/search-selector.tsx
@@ -1,7 +1,7 @@
 import Nav from 'react-bootstrap/Nav';
 import { useSearchParams } from 'react-router-dom';
 
-type SearchView = 't2b' | 'b2b' | 't2bs';
+type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding';
 
 type Props = {
   view: SearchView;
@@ -45,6 +45,16 @@ export const SearchSelector = (props: Props) => {
           >
             Text-to-BEDset
           
+           {
+              params.set('view', 'embedding');
+              params.delete('q');
+              setParams(params);
+              setView('embedding');
+            }}
+          >
+            Embedding Atlas
+          
         
       

     

diff --git a/ui/src/contexts/mosaic-coordinator-context.tsx b/ui/src/contexts/mosaic-coordinator-context.tsx
new file mode 100644
index 00000000..0da56cc1
--- /dev/null
+++ b/ui/src/contexts/mosaic-coordinator-context.tsx
@@ -0,0 +1,64 @@
+import { createContext, useContext, useMemo, useRef, ReactNode } from 'react';
+import * as vg from '@uwdata/vgplot';
+
+interface MosaicCoordinatorContextType {
+  getCoordinator: () => vg.Coordinator;
+  initializeData: () => Promise;
+}
+
+const MosaicCoordinatorContext = createContext(null);
+
+export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode }) => {
+  const coordinatorRef = useRef(null);
+  const dataInitializedRef = useRef(false);
+
+  const getCoordinator = () => {
+    if (!coordinatorRef.current) {
+      coordinatorRef.current = new vg.Coordinator(vg.wasmConnector());
+    }
+    return coordinatorRef.current;
+  };
+
+  const initializeData = async () => {
+    if (dataInitializedRef.current) {
+      return; // Already initialized
+    }
+
+    const coordinator = getCoordinator();
+    const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json';
+
+    await coordinator.exec([
+      vg.sql`CREATE OR REPLACE TABLE data AS
+            SELECT
+              unnest(nodes, recursive := true)
+            FROM read_json_auto('${url}')`,
+      vg.sql`CREATE OR REPLACE TABLE data AS
+            SELECT
+              *,
+              (DENSE_RANK() OVER (ORDER BY assay) - 1)::INTEGER AS assay_category,
+              (DENSE_RANK() OVER (ORDER BY cell_line) - 1)::INTEGER AS cell_line_category
+            FROM data` as any
+    ]);
+
+    dataInitializedRef.current = true;
+  };
+
+  const value = useMemo(() => ({ getCoordinator, initializeData }), []);
+  return (
+    
+      {children}
+    
+  );
+}
+
+export const useMosaicCoordinator = () => {
+  const context = useContext(MosaicCoordinatorContext);
+  if (!context) {
+    throw new Error('useMosaicCoordinator must be used within MosaicCoordinatorProvider');
+  }
+  return {
+    coordinator: context.getCoordinator(),
+    initializeData: context.initializeData
+  };
+};
+
diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index df411949..548e1cb3 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -10,6 +10,7 @@ import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
 import { UMAPGraph } from './pages/visualization.tsx';
 import { HelmetProvider } from 'react-helmet-async';
+import { MosaicCoordinatorProvider } from './contexts/mosaic-coordinator-context.tsx';
 
 // css stuff
 import 'bootstrap/dist/css/bootstrap.min.css';
@@ -88,8 +89,10 @@ ReactDOM.createRoot(document.getElementById('root')!).render(
       
         
           
-            
-            
+            
+              
+              
+            
           
           
         
diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx
index 8b2857ee..c3bb980a 100644
--- a/ui/src/pages/bed-splash.tsx
+++ b/ui/src/pages/bed-splash.tsx
@@ -28,7 +28,7 @@ export const BedSplash = () => {
   const params = useParams();
   const bedId = params.id;
 
-  const [showNeighbors, setShowNeighbors] = useState(true);
+  const [showNeighbors, setShowNeighbors] = useState(false);
 
   const {
     isLoading,
diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx
index d2c2f49b..ab1da7ab 100644
--- a/ui/src/pages/search.tsx
+++ b/ui/src/pages/search.tsx
@@ -7,10 +7,11 @@ import { SearchSelector } from '../components/search/search-selector';
 import { Text2Bed } from '../components/search/text2bed/text2bed';
 import { Bed2Bed } from '../components/search/bed2bed/bed2bed';
 import { Text2BedSet } from '../components/search/text2bedset';
+import { BEDAtlas } from '../components/search/bed-atlas.tsx';
 
 import { SearchViewProvider } from '../contexts/search-view-context.tsx';
 
-type SearchView = 't2b' | 'b2b' | 't2bs';
+type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding';
 
 export const SearchPage = () => {
   const [searchParams] = useSearchParams();
@@ -31,6 +32,8 @@ export const SearchPage = () => {
           
         ) : searchView === 't2bs' ? (
           
+        ) : searchView === 'embedding' ? (
+          
         ) : (
           
Unknown searchView selected.

         )}

From 690c84515a07076f5207f70c319d9069b68ae5ac Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Thu, 30 Oct 2025 20:54:48 -0400
Subject: [PATCH 24/65] Added Analyze button to bed page + improvements in
 analytics page

---
 ui/src/components/bed-splash-components/header.tsx |  6 ++++++
 ui/src/pages/bed-analytics.tsx                     | 11 ++++++++---
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/ui/src/components/bed-splash-components/header.tsx b/ui/src/components/bed-splash-components/header.tsx
index 7a04d4a1..c705f9f3 100644
--- a/ui/src/components/bed-splash-components/header.tsx
+++ b/ui/src/components/bed-splash-components/header.tsx
@@ -81,6 +81,12 @@ export const BedSplashHeader = (props: Props) => {
               
             
           }
+          
+            
+          
           
             
-                      
+                      
-                      
+                      
-                      
+                      
-                      
+                      

           
         
                     

                       Identifier{rs.digest}{rs.identifier}
                     

                     

                       Mean region width{rs.mean_region_width}{rs.meanRegionWidth}
                     

                     

                       Total number of regions{rs.number_of_regions}{rs.numberOfRegions}
                     

                     

                       Total number of nucleotides{rs.total_nucleotides}{rs.nucleotidesLength}
                     

                     
                   

@@ -290,9 +289,16 @@ export const BEDAnalytics = () => {
                 

                 

                   {rs && (
+                    // 

+                    //   
Region Distribution Data

+                    //   
+                    //     {JSON.stringify(rs.calculateRegionDistribution(300), null, 2)}
+                    //   

+                    // 

                     

                       
                     

                   )}

From 7c651d44672620acff9e59a6407c276c110fd137 Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Fri, 31 Oct 2025 20:01:36 -0400
Subject: [PATCH 26/65] replace 3d with embedding atlas component

---
 ui/package-lock.json                          |   8 +-
 ui/package.json                               |   2 +-
 .../bed-splash-components/bad-atlas.tsx       |  55 +++---
 ui/src/components/layout.tsx                  |  25 ++-
 ui/src/components/search/bed-atlas.tsx        |   1 +
 ui/src/components/search/search-selector.tsx  |  12 +-
 ui/src/main.tsx                               |   4 +-
 ui/src/pages/bed-atlas-full.tsx               |  44 +++++
 ui/src/pages/search.tsx                       |   5 +-
 ui/src/pages/visualization.tsx                | 177 ------------------
 10 files changed, 104 insertions(+), 229 deletions(-)
 create mode 100644 ui/src/pages/bed-atlas-full.tsx
 delete mode 100644 ui/src/pages/visualization.tsx

diff --git a/ui/package-lock.json b/ui/package-lock.json
index b69667fb..aaa26af8 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -18,7 +18,7 @@
         "chart.js": "^4.4.2",
         "chartjs-chart-error-bars": "^4.4.0",
         "chartjs-plugin-datalabels": "^2.2.0",
-        "embedding-atlas": "^0.11.0",
+        "embedding-atlas": "^0.12.0",
         "framer-motion": "^11.0.20",
         "js-yaml": "^4.1.0",
         "react": "^18.2.0",
@@ -3748,9 +3748,9 @@
       "license": "ISC"
     },
     "node_modules/embedding-atlas": {
-      "version": "0.11.0",
-      "resolved": "https://registry.npmjs.org/embedding-atlas/-/embedding-atlas-0.11.0.tgz",
-      "integrity": "sha512-jA/mzhCOOmRfcU1wzqaToKPfFpHQ2V241sVchoF4fP8Br3wJf7bvM5PwjkIAc9fDxrx5RxQna76Vzr93ht2gyg==",
+      "version": "0.12.0",
+      "resolved": "https://registry.npmjs.org/embedding-atlas/-/embedding-atlas-0.12.0.tgz",
+      "integrity": "sha512-DPsKR4uTsMseCCb7xAl4z9daj6MYasXGfk4aXI3vCqF73q2kQ4oe1Pp4GCe6sYpbAR3WpHDlAU9reC52piepMw==",
       "license": "MIT",
       "peerDependencies": {
         "@uwdata/mosaic-core": ">=0.19.0",
diff --git a/ui/package.json b/ui/package.json
index a6a7caac..10433646 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -22,7 +22,7 @@
     "chart.js": "^4.4.2",
     "chartjs-chart-error-bars": "^4.4.0",
     "chartjs-plugin-datalabels": "^2.2.0",
-    "embedding-atlas": "^0.11.0",
+    "embedding-atlas": "^0.12.0",
     "framer-motion": "^11.0.20",
     "js-yaml": "^4.1.0",
     "react": "^18.2.0",
diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx
index bcbe8676..22e949a0 100644
--- a/ui/src/components/bed-splash-components/bad-atlas.tsx
+++ b/ui/src/components/bed-splash-components/bad-atlas.tsx
@@ -125,6 +125,11 @@ export const BADAtlas = (props: Props) => {
 
     let result;
 
+    // Build filter clause if a legend filter is active
+    const filterClause = filterSelection
+      ? ` AND ${colorGrouping} = '${filterSelection.category}'`
+      : '';
+
     // Check if rectangle selection (bounding box)
     if (typeof value === 'object' && 'xMin' in value) {
       result = await coordinator.query(
@@ -135,7 +140,7 @@ export const BADAtlas = (props: Props) => {
           id as identifier,
           {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
          FROM data
-         WHERE x >= ${value.xMin} AND x <= ${value.xMax} AND y >= ${value.yMin} AND y <= ${value.yMax}`,
+         WHERE x >= ${value.xMin} AND x <= ${value.xMax} AND y >= ${value.yMin} AND y <= ${value.yMax}${filterClause}`,
         { type: 'json' }
       ) as any[];
     }
@@ -152,7 +157,7 @@ export const BADAtlas = (props: Props) => {
       // Only fetch x, y, identifier for filtering, then get full data for matches
       const candidates: any = await coordinator.query(
         `SELECT x, y, id as identifier FROM data
-         WHERE x >= ${xMin} AND x <= ${xMax} AND y >= ${yMin} AND y <= ${yMax}`,
+         WHERE x >= ${xMin} AND x <= ${xMax} AND y >= ${yMin} AND y <= ${yMax}${filterClause}`,
         { type: 'json' }
       );
 
@@ -171,7 +176,7 @@ export const BADAtlas = (props: Props) => {
             id as identifier,
             {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
            FROM data
-           WHERE id IN (${filteredIds})`,
+           WHERE id IN (${filteredIds})${filterClause}`,
           { type: 'json' }
         ) as any[];
       } else {
@@ -179,33 +184,31 @@ export const BADAtlas = (props: Props) => {
       }
     }
 
-    if (result && result.length > 0) {
-      // Always ensure initialPoint is included
-      const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint?.identifier);
-      let finalPoints = hasInitialPoint ? result : (initialPoint ? [initialPoint, ...result] : result);
+    const resultArray = result || [];
+    const hasInitialPoint = resultArray.length > 0 && resultArray.some((p: any) => p.identifier === initialPoint?.identifier);
+    let finalPoints = hasInitialPoint ? resultArray : (initialPoint ? [initialPoint, ...resultArray] : resultArray);
 
-      if (showNeighbors && neighborIDs && neighborIDs.length > 0) {
-        const selectedIds = new Set(finalPoints.map((p: any) => p.identifier));
-        const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id));
+    if (showNeighbors && neighborIDs && neighborIDs.length > 0) {
+      const selectedIds = new Set(finalPoints.map((p: any) => p.identifier));
+      const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id));
 
-        if (missingNeighborIds.length > 0) { // fetch missing neighbor points
-          const neighborPoints = await coordinator.query(
-            `SELECT
-              x, y,
-              ${colorGrouping} as category,
-              name as text,
-              id as identifier,
-              {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
-             FROM data
-             WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`,
-            { type: 'json' }
-          ) as any[];
-          finalPoints = [...finalPoints, ...neighborPoints];
-        }
+      if (missingNeighborIds.length > 0) { // fetch missing neighbor points
+        const neighborPoints = await coordinator.query(
+          `SELECT
+            x, y,
+            ${colorGrouping} as category,
+            name as text,
+            id as identifier,
+            {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
+           FROM data
+           WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`,
+          { type: 'json' }
+        ) as any[];
+        finalPoints = [...finalPoints, ...neighborPoints];
       }
-
-      setSelectedPoints(finalPoints);
     }
+
+    setSelectedPoints(finalPoints);
   };
 
   const fetchLegendItems = async (coordinator: any) => {
diff --git a/ui/src/components/layout.tsx b/ui/src/components/layout.tsx
index f006bcec..df2db937 100644
--- a/ui/src/components/layout.tsx
+++ b/ui/src/components/layout.tsx
@@ -12,6 +12,7 @@ type LayoutProps = {
   fullWidth?: boolean;
   footer?: boolean;
   fullHeight?: boolean;
+  flexLayout?: boolean;
 };
 
 const Footer = () => {
@@ -67,16 +68,32 @@ const Footer = () => {
 };
 
 export const Layout = (props: LayoutProps) => {
-  const { children, title, description, image, footer, fullHeight } = props;
-  const mainContainerClass = fullHeight ? 'container min-h-screen' : 'container';
+  const { children, title, description, image, footer, fullHeight, fullWidth, flexLayout } = props;
+  
+  if (flexLayout) {
+    return (
+      
+        
+        

+          

+            

+          
{children}

+        

+        {!!footer && 
}
+      
+    );
+  }
+
+  const fluidContainer = `${fullWidth ? 'container-fluid' : 'container'}`
   return (
     
       
       

         

-      
{children}

-      {footer === true && 
}
+      
{children}

+      {!!footer && 
}
     
   );
 };
diff --git a/ui/src/components/search/bed-atlas.tsx b/ui/src/components/search/bed-atlas.tsx
index d7799159..ded5e8b5 100644
--- a/ui/src/components/search/bed-atlas.tsx
+++ b/ui/src/components/search/bed-atlas.tsx
@@ -1,6 +1,7 @@
 import { EmbeddingAtlas } from 'embedding-atlas/react';
 import { useEffect, useState } from 'react';
 import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
+
 type Props = {
   bedId?: string;
   neighbors?: any;
diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx
index 94ffa07f..41cef61c 100644
--- a/ui/src/components/search/search-selector.tsx
+++ b/ui/src/components/search/search-selector.tsx
@@ -1,7 +1,7 @@
 import Nav from 'react-bootstrap/Nav';
 import { useSearchParams } from 'react-router-dom';
 
-type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding';
+type SearchView = 't2b' | 'b2b' | 't2bs';
 
 type Props = {
   view: SearchView;
@@ -45,16 +45,6 @@ export const SearchSelector = (props: Props) => {
           >
             Text-to-BEDset
           
-           {
-              params.set('view', 'embedding');
-              params.delete('q');
-              setParams(params);
-              setView('embedding');
-            }}
-          >
-            Embedding Atlas
-          
         
       

     

diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index 548e1cb3..5443ea04 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -8,7 +8,7 @@ import { BedCartProvider } from './contexts/bedcart-context.tsx';
 import toast, { Toaster } from 'react-hot-toast';
 import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
-import { UMAPGraph } from './pages/visualization.tsx';
+import { BEDAtlasFull } from './pages/bed-atlas-full.tsx';
 import { HelmetProvider } from 'react-helmet-async';
 import { MosaicCoordinatorProvider } from './contexts/mosaic-coordinator-context.tsx';
 
@@ -78,7 +78,7 @@ const router = createBrowserRouter([
   },
   {
     path: '/umap',
-    element: ,
+    element: ,
   },
 ]);
 
diff --git a/ui/src/pages/bed-atlas-full.tsx b/ui/src/pages/bed-atlas-full.tsx
new file mode 100644
index 00000000..ac94e22b
--- /dev/null
+++ b/ui/src/pages/bed-atlas-full.tsx
@@ -0,0 +1,44 @@
+import { EmbeddingAtlas } from 'embedding-atlas/react';
+import { useEffect, useState } from 'react';
+import { useMosaicCoordinator } from '../contexts/mosaic-coordinator-context';
+import { Layout } from '../components/layout';
+
+
+export const BEDAtlasFull: React.FC = () => {
+  const [isReady, setIsReady] = useState(false);
+  const { coordinator, initializeData } = useMosaicCoordinator();
+
+  useEffect(() => {
+    initializeData().then(() => setIsReady(true));
+  }, []);
+
+  return (
+    
+      {isReady ? (
+        

+          

+            
+          

+        

+    ) : (
+      

+        

+          Loading...
+        

+      

+    )}
+
+    
+  );
+};
\ No newline at end of file
diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx
index ab1da7ab..d2c2f49b 100644
--- a/ui/src/pages/search.tsx
+++ b/ui/src/pages/search.tsx
@@ -7,11 +7,10 @@ import { SearchSelector } from '../components/search/search-selector';
 import { Text2Bed } from '../components/search/text2bed/text2bed';
 import { Bed2Bed } from '../components/search/bed2bed/bed2bed';
 import { Text2BedSet } from '../components/search/text2bedset';
-import { BEDAtlas } from '../components/search/bed-atlas.tsx';
 
 import { SearchViewProvider } from '../contexts/search-view-context.tsx';
 
-type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding';
+type SearchView = 't2b' | 'b2b' | 't2bs';
 
 export const SearchPage = () => {
   const [searchParams] = useSearchParams();
@@ -32,8 +31,6 @@ export const SearchPage = () => {
           
         ) : searchView === 't2bs' ? (
           
-        ) : searchView === 'embedding' ? (
-          
         ) : (
           
Unknown searchView selected.

         )}
diff --git a/ui/src/pages/visualization.tsx b/ui/src/pages/visualization.tsx
deleted file mode 100644
index fa5434df..00000000
--- a/ui/src/pages/visualization.tsx
+++ /dev/null
@@ -1,177 +0,0 @@
-import React, { useRef, useState, useEffect } from 'react';
-import ForceGraph3D from 'react-force-graph-3d';
-// import graphData from './output.json';
-import { Link } from 'react-router-dom';
-import { useUmapEmbeddings } from '../queries/useUmapEmbeddings.ts';
-import { useNavigate, useLocation } from 'react-router-dom';
-
-export interface GraphNode {
-  id: string;
-  name: string;
-  description: string;
-  cell_line: string;
-  assay?: string;
-  x: number;
-  y: number;
-  z: number;
-}
-
-type ColorBy = 'cell_line' | 'assay';
-
-export const UMAPGraph: React.FC = () => {
-  const { data: umap_data, isLoading, error } = useUmapEmbeddings();
-  const fgRef = useRef();
-  const [searchId, setSearchId] = useState('');
-  const [message, setMessage] = useState('');
-  const navigate = useNavigate();
-  const location = useLocation();
-  const [colorByOption, setColorByOption] = useState('cell_line');
-
-
-  useEffect(() => {
-    const queryParams = new URLSearchParams(location.search);
-    const initialSearchId = queryParams.get('searchId');
-    if (initialSearchId) {
-      setSearchId(initialSearchId);
-      const timer = setTimeout(() => {
-        handleSearch();
-      }, 1000); // Give time for the graph to initialize
-      return () => clearTimeout(timer);
-    }
-  }, [location.search, umap_data]);
-
-  const handleSearch = () => {
-
-    if (!umap_data) return;
-    const node = graphDataWithoutLinks.nodes.find((n: GraphNode) => n.id === searchId);
-
-    if (node && fgRef.current) {
-      fgRef.current.cameraPosition(
-        { x: node.x, y: node.y, z: node.z + 300 }, // zoom in 300 units away
-        node,
-        2000, // animate over 2 seconds
-      );
-      setMessage(`Found: ${node.id}`);
-      navigate(`?searchId=${node.id}`);
-    } else {
-
-      fgRef.current.cameraPosition(
-        { x: 0, y: 0, z: 1000 }, // reset to default center position
-        { x: 0, y: 0, z: 0 }, // look at the center
-        2000, // animate over 2 seconds
-      );
-      if (!searchId) {
-        setMessage('');
-      } else {
-        setMessage(`Node with ID ${searchId} not found.`);
-      }
-      // setMessage('BED file not found or search is empty.');
-      navigate(`?searchId=${node.id}`);
-    }
-  };
-
-  if (isLoading) {
-    return 
Loading data...
;
-  }
-
-  if (error) {
-    return 
Error loading data: {error.message}
;
-  }
-
-  const graphDataWithoutLinks = {
-    nodes: umap_data.nodes.map((node: GraphNode) => ({
-      ...node,
-      x: node.x,
-      y: node.y,
-      z: node.z,
-    })),
-    links: [],
-  };
-
-  return (
-    

-
-      

-        

-          

-             setColorByOption('cell_line')}
-            />
-            
-
-             setColorByOption('assay')}
-            />
-            
-          

-        

-        

-           setSearchId(e.target.value)}
-            onKeyDown={e => e.key === 'Enter' && handleSearch()}
-            className="form-control me-2"
-          />
-          
-        

-
-        

-          {message && 
{message}
}
-        

-      

-
-       (
-          `
${node.id}
cell_line: ${node.cell_line}
assay: ${node.assay}
${node.description}
`
-        )}
-        nodeAutoColorBy={colorByOption}
-        nodeRelSize={60}
-        enableNodeDrag={false}
-        onNodeClick={(node: GraphNode) => {
-          if (node.id) {
-            // const url = `https://bedbase.org/bed/${node.id}`;
-            // window.open(url, '_blank');
-            // navigator.clipboard.writeText(url).catch(console.error);
-            setSearchId(node.id);
-            handleSearch();
-            setMessage(`Clicked on: ${node.id} \n ${node.cell_line} <\n  ${node.assay}`);
-          }
-        }}
-      />
-      

-        
-          BEDbase Logo
-        
-
-      

-    

-
-  );
-};
\ No newline at end of file

From 2c19557c91389181d97abcc73521dd6e8340b9ab Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 14:37:33 -0500
Subject: [PATCH 27/65] updated ui dependencies

---
 ui/package-lock.json | 4 ++--
 ui/package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index b80b72b1..0ce60290 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -8,7 +8,7 @@
       "name": "bedhost-ui-2",
       "version": "0.0.0",
       "dependencies": {
-        "@databio/gtars": "file:../../gtars/gtars-wasm/pkg",
+        "@databio/gtars": "^0.5.2",
         "@tanstack/react-query": "^5.28.0",
         "@tanstack/react-query-devtools": "^5.28.0",
         "@tanstack/react-table": "^8.15.3",
@@ -56,7 +56,7 @@
     },
     "../../gtars/gtars-wasm/pkg": {
       "name": "@databio/gtars",
-      "version": "0.5.1"
+      "version": "0.5.2"
     },
     "node_modules/@babel/code-frame": {
       "version": "7.27.1",
diff --git a/ui/package.json b/ui/package.json
index 78ba8c5f..0d73b9d5 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -12,7 +12,7 @@
     "generate-types-local": "npx openapi-typescript http://localhost:8000/openapi.json -o bedbase-types.d.ts"
   },
   "dependencies": {
-    "@databio/gtars": "file:../../gtars/gtars-wasm/pkg",
+    "@databio/gtars": "^0.5.2",
     "@tanstack/react-query": "^5.28.0",
     "@tanstack/react-query-devtools": "^5.28.0",
     "@tanstack/react-table": "^8.15.3",

From 343eef0b26b7e773adc97f3ec09a903b9aef272f Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 14:42:03 -0500
Subject: [PATCH 28/65] updated ui dependencies and fixed errors

---
 ui/package-lock.json                                |  7 +++++++
 ui/package.json                                     |  1 +
 .../bed-analytics-components/bed-plots.tsx          |  7 +++----
 .../chromosome-stats-panel.tsx                      | 13 ++++---------
 4 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 0ce60290..634059e1 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -12,6 +12,7 @@
         "@tanstack/react-query": "^5.28.0",
         "@tanstack/react-query-devtools": "^5.28.0",
         "@tanstack/react-table": "^8.15.3",
+        "@types/pako": "^2.0.4",
         "@uidotdev/usehooks": "^2.4.1",
         "axios": "^1.8.2",
         "bootstrap": "^5.3.3",
@@ -2154,6 +2155,12 @@
         "undici-types": "~6.21.0"
       }
     },
+    "node_modules/@types/pako": {
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/@types/pako/-/pako-2.0.4.tgz",
+      "integrity": "sha512-VWDCbrLeVXJM9fihYodcLiIv0ku+AlOa/TQ1SvYOaBuyrSKgEcro95LJyIsJ4vSo6BXIxOKxiJAat04CmST9Fw==",
+      "license": "MIT"
+    },
     "node_modules/@types/prop-types": {
       "version": "15.7.15",
       "resolved": "https://registry.npmjs.org/@types/prop-types/-/prop-types-15.7.15.tgz",
diff --git a/ui/package.json b/ui/package.json
index 0d73b9d5..351c60d4 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -16,6 +16,7 @@
     "@tanstack/react-query": "^5.28.0",
     "@tanstack/react-query-devtools": "^5.28.0",
     "@tanstack/react-table": "^8.15.3",
+    "@types/pako": "^2.0.4",
     "@uidotdev/usehooks": "^2.4.1",
     "axios": "^1.8.2",
     "bootstrap": "^5.3.3",
diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index 70a0f3c3..5ca1d135 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -9,7 +9,7 @@ type DistributionSpecDataPoint = {
   end: number;
   n: number;
   rid: number;
-  
+
 }
 
 interface BedPlotsProps {
@@ -19,14 +19,13 @@ interface BedPlotsProps {
 const distributionSpec = (data: DistributionSpecDataPoint[]) => {
 
   // Transform data to match the new schema requirements
-  const transformedData = data.map((item: DistributionSpecDataPoint, i: number) => ({
+  const transformedData = data.map((item: DistributionSpecDataPoint) => ({
     chr: item.chr,
     withinGroupID: item.rid,
     N: item.n,
     start: item.start,
     end: item.end,
   }));
-
   return {
     $schema: 'https://vega-github.io/schema/vega-lite/v6.json',
     title: {
@@ -62,7 +61,7 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
     },
     encoding: {
       row: {
-        title: "Chromosome",
+        title: 'Chromosome',
         field: 'chr',
         header: {
           labelAlign: 'right',
diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index 72e64cf2..26d22cc0 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -11,7 +11,8 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
   if (!calc) return null;
 
   const statsEntries = Array.from(calc.entries())
-    .map(([chrom, stats]: [unknown, ChromosomeStatistics]) => {
+    .map((entry) => {
+      const [chrom, stats] = entry as [unknown, ChromosomeStatistics];
       const cs = stats as ChromosomeStatistics;
       const row = {
         chromosome: String(chrom),
@@ -29,20 +30,14 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
         /* ignore */
       }
       return row;
-    })
-    .sort((a, b) =>
-      a.chromosome.localeCompare(b.chromosome, undefined, {
-        numeric: true,
-        sensitivity: 'base',
-      }),
-    );
+    });
 
   return (
     

       {/*This section is AI rendered. It provides statistics on number of regions per chromosome.*/}
       

         
Number of regions per chromosome: 

-        

+        

           
Date: Tue, 4 Nov 2025 15:11:53 -0500
Subject: [PATCH 29/65] Updated ui lock

---
 ui/package-lock.json | 7704 ------------------------------------------
 1 file changed, 7704 deletions(-)
 delete mode 100644 ui/package-lock.json

diff --git a/ui/package-lock.json b/ui/package-lock.json
deleted file mode 100644
index 634059e1..00000000
--- a/ui/package-lock.json
+++ /dev/null
@@ -1,7704 +0,0 @@
-{
-  "name": "bedhost-ui-2",
-  "version": "0.0.0",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "bedhost-ui-2",
-      "version": "0.0.0",
-      "dependencies": {
-        "@databio/gtars": "^0.5.2",
-        "@tanstack/react-query": "^5.28.0",
-        "@tanstack/react-query-devtools": "^5.28.0",
-        "@tanstack/react-table": "^8.15.3",
-        "@types/pako": "^2.0.4",
-        "@uidotdev/usehooks": "^2.4.1",
-        "axios": "^1.8.2",
-        "bootstrap": "^5.3.3",
-        "bootstrap-icons": "^1.11.3",
-        "chart.js": "^4.4.2",
-        "chartjs-chart-error-bars": "^4.4.0",
-        "chartjs-plugin-datalabels": "^2.2.0",
-        "framer-motion": "^11.0.20",
-        "js-yaml": "^4.1.0",
-        "pako": "^2.1.0",
-        "react": "^18.2.0",
-        "react-bootstrap": "^2.10.1",
-        "react-chartjs-2": "^5.2.0",
-        "react-dom": "^18.2.0",
-        "react-dropzone": "^14.2.3",
-        "react-force-graph-3d": "^1.27.0",
-        "react-helmet-async": "^2.0.4",
-        "react-hot-toast": "^2.4.1",
-        "react-markdown": "^9.0.1",
-        "react-router-dom": "^7.5.2",
-        "rehype-highlight": "^7.0.0",
-        "three": "^0.177.0",
-        "vega-embed": "^7.0.2",
-        "vite-plugin-top-level-await": "^1.6.0",
-        "vite-plugin-wasm": "^3.5.0"
-      },
-      "devDependencies": {
-        "@types/js-yaml": "^4.0.9",
-        "@types/node": "^20.11.27",
-        "@types/react": "^18.2.64",
-        "@types/react-dom": "^18.2.21",
-        "@typescript-eslint/eslint-plugin": "^7.1.1",
-        "@typescript-eslint/parser": "^7.1.1",
-        "@vitejs/plugin-react": "^4.4.1",
-        "eslint": "^8.57.0",
-        "eslint-plugin-react-hooks": "^4.6.0",
-        "eslint-plugin-react-refresh": "^0.4.5",
-        "sass": "^1.72.0",
-        "typescript": "^5.2.2",
-        "vite": "^6.3.6"
-      }
-    },
-    "../../gtars/gtars-wasm/pkg": {
-      "name": "@databio/gtars",
-      "version": "0.5.2"
-    },
-    "node_modules/@babel/code-frame": {
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-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/core": {
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-      "version": "22.0.0",
-      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-22.0.0.tgz",
-      "integrity": "sha512-rwu/ClNdSMpkSrUb+d6BRsSkLUq1fmfsY6TOpYzTwvwkg1/NRG85KBy3kq++A8LKQwX6lsu+aWad+2khvuXrqw==",
-      "license": "ISC",
-      "peer": true,
-      "engines": {
-        "node": "^20.19.0 || ^22.12.0 || >=23"
-      }
-    },
-    "node_modules/yocto-queue": {
-      "version": "0.1.0",
-      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
-      "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
-    "node_modules/zwitch": {
-      "version": "2.0.4",
-      "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
-      "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
-      "license": "MIT",
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/wooorm"
-      }
-    }
-  }
-}

From 846320319088d1c7ba5bfb8ff93be2f690090c2d Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 16:06:42 -0500
Subject: [PATCH 30/65] added gtars init

---
 ui/src/main.tsx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index f906399a..7f8dfe27 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -10,6 +10,7 @@ import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
 import { UMAPGraph } from './pages/visualization.tsx';
 import { BEDAnalytics } from './pages/bed-analytics.tsx';
+import { init } from '@databio/gtars'
 import { HelmetProvider } from 'react-helmet-async';
 
 // css stuff
@@ -87,6 +88,9 @@ const router = createBrowserRouter([
   },
 ]);
 
+// initialize gtars:
+init();
+
 // entry point
 ReactDOM.createRoot(document.getElementById('root')!).render(
   

From a66aa7b6966eeabc68c6598f67790669ac68f487 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 17:26:19 -0500
Subject: [PATCH 31/65] fixing wasm

---
 ui/src/main.tsx | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index 7f8dfe27..7b56ddc5 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -10,7 +10,7 @@ import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
 import { UMAPGraph } from './pages/visualization.tsx';
 import { BEDAnalytics } from './pages/bed-analytics.tsx';
-import { init } from '@databio/gtars'
+import init from '@databio/gtars';
 import { HelmetProvider } from 'react-helmet-async';
 
 // css stuff
@@ -37,14 +37,16 @@ const queryClient = new QueryClient({
     onError: (error: any) => {
       if (error.response && error.response.status === 413) {
         toast.error(`${error.response.data.detail}`);
-      return;}
+        return;
+      }
       if (error.response && error.response.status === 415) {
         toast.error(`${error.response.data.detail}`);
-      return;}
+        return;
+      }
       //
       // console.error(error);
       // toast.error(`Something went wrong: ${error.message}`);
-    }
+    },
   }),
 });
 

From 85cec759132e4269bbfe629cbed59c78af4ff2cf Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Fri, 7 Nov 2025 11:10:17 -0500
Subject: [PATCH 32/65] rename some files and components

---
 ui/src/components/search/bed-atlas.tsx        | 52 -----------
 .../components/umap/bed-embedding-atlas.tsx   | 88 +++++++++++++++++++
 .../bed-embedding-view.tsx}                   |  8 +-
 ui/src/main.tsx                               |  4 +-
 ui/src/pages/bed-atlas-full.tsx               | 44 ----------
 ui/src/pages/bed-splash.tsx                   |  6 +-
 ui/src/pages/bed-umap.tsx                     | 16 ++++
 7 files changed, 112 insertions(+), 106 deletions(-)
 delete mode 100644 ui/src/components/search/bed-atlas.tsx
 create mode 100644 ui/src/components/umap/bed-embedding-atlas.tsx
 rename ui/src/components/{bed-splash-components/bad-atlas.tsx => umap/bed-embedding-view.tsx} (98%)
 delete mode 100644 ui/src/pages/bed-atlas-full.tsx
 create mode 100644 ui/src/pages/bed-umap.tsx

diff --git a/ui/src/components/search/bed-atlas.tsx b/ui/src/components/search/bed-atlas.tsx
deleted file mode 100644
index ded5e8b5..00000000
--- a/ui/src/components/search/bed-atlas.tsx
+++ /dev/null
@@ -1,52 +0,0 @@
-import { EmbeddingAtlas } from 'embedding-atlas/react';
-import { useEffect, useState } from 'react';
-import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
-
-type Props = {
-  bedId?: string;
-  neighbors?: any;
-}
-
-export const BEDAtlas = (props: Props) => {
-  const {} = props;
-
-  const [isReady, setIsReady] = useState(false);
-  const { coordinator, initializeData } = useMosaicCoordinator();
-
-  useEffect(() => {
-    initializeData().then(() => setIsReady(true));
-  }, []);
-
-  return (
-    <>
-      {isReady ? (
-        

-          

-            

-              

-                
-              

-            

-          

-        

-      ) : (
-        

-          

-            Loading...
-          

-        

-      )}
-    
-  );
-}
\ No newline at end of file
diff --git a/ui/src/components/umap/bed-embedding-atlas.tsx b/ui/src/components/umap/bed-embedding-atlas.tsx
new file mode 100644
index 00000000..39701d2d
--- /dev/null
+++ b/ui/src/components/umap/bed-embedding-atlas.tsx
@@ -0,0 +1,88 @@
+import { EmbeddingAtlas } from 'embedding-atlas/react';
+import { useEffect, useState } from 'react';
+import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
+
+type Props = {
+  bedId?: string;
+  neighbors?: any;
+  container?: boolean;
+  width?: string;
+  height?: string;
+}
+
+export const BEDEmbeddingAtlas = (props: Props) => {
+  const {container, width, height} = props;
+
+  const [isReady, setIsReady] = useState(false);
+  const { coordinator, initializeData } = useMosaicCoordinator();
+
+  useEffect(() => {
+    initializeData().then(() => setIsReady(true));
+  }, []);
+
+  return (
+    container ? (
+      <>
+        {isReady ? (
+          

+            

+              

+                

+                  
+                

+              

+            

+          

+        ) : (
+          

+            

+              Loading...
+            

+          

+        )}
+      
+    ) : (
+      <>
+        {isReady ? (
+          

+            

+               console.log(e)}
+                onExportSelection={async (predicate, format) => {
+                  console.log('Export selection:', predicate, format);
+                }}
+              />
+            

+          

+      ) : (
+        

+          

+            Loading...
+          

+        

+      )}
+      
+    )
+  );
+}
diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/umap/bed-embedding-view.tsx
similarity index 98%
rename from ui/src/components/bed-splash-components/bad-atlas.tsx
rename to ui/src/components/umap/bed-embedding-view.tsx
index 22e949a0..40ae689b 100644
--- a/ui/src/components/bed-splash-components/bad-atlas.tsx
+++ b/ui/src/components/umap/bed-embedding-view.tsx
@@ -5,7 +5,7 @@ import * as vg from '@uwdata/vgplot'
 import { isPointInPolygon, tableau20 } from '../../utils';
 import { useBedCart } from '../../contexts/bedcart-context';
 import { components } from '../../../bedbase-types';
-import { AtlasTooltip } from './atlas-tooltip';
+import { AtlasTooltip } from '../bed-splash-components/atlas-tooltip';
 import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
 
 type SearchResponse = components['schemas']['BedListSearchResult'];
@@ -16,7 +16,7 @@ type Props = {
   showNeighbors?: boolean;
 }
 
-export const BADAtlas = (props: Props) => {
+export const BEDEmbeddingView = (props: Props) => {
   const { bedId, neighbors, showNeighbors } = props;
   const { coordinator, initializeData } = useMosaicCoordinator();
   const { addBedToCart } = useBedCart();
@@ -125,7 +125,7 @@ export const BADAtlas = (props: Props) => {
 
     let result;
 
-    // Build filter clause if a legend filter is active
+    // filter clause prevents selecting points that are not within a selected legend category
     const filterClause = filterSelection
       ? ` AND ${colorGrouping} = '${filterSelection.category}'`
       : '';
@@ -454,4 +454,4 @@ export const BADAtlas = (props: Props) => {
       )}
     
   );
-}
\ No newline at end of file
+}
diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index 5443ea04..5bf18a37 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -8,7 +8,7 @@ import { BedCartProvider } from './contexts/bedcart-context.tsx';
 import toast, { Toaster } from 'react-hot-toast';
 import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
-import { BEDAtlasFull } from './pages/bed-atlas-full.tsx';
+import { BEDUmap } from './pages/bed-umap.tsx';
 import { HelmetProvider } from 'react-helmet-async';
 import { MosaicCoordinatorProvider } from './contexts/mosaic-coordinator-context.tsx';
 
@@ -78,7 +78,7 @@ const router = createBrowserRouter([
   },
   {
     path: '/umap',
-    element: ,
+    element: ,
   },
 ]);
 
diff --git a/ui/src/pages/bed-atlas-full.tsx b/ui/src/pages/bed-atlas-full.tsx
deleted file mode 100644
index ac94e22b..00000000
--- a/ui/src/pages/bed-atlas-full.tsx
+++ /dev/null
@@ -1,44 +0,0 @@
-import { EmbeddingAtlas } from 'embedding-atlas/react';
-import { useEffect, useState } from 'react';
-import { useMosaicCoordinator } from '../contexts/mosaic-coordinator-context';
-import { Layout } from '../components/layout';
-
-
-export const BEDAtlasFull: React.FC = () => {
-  const [isReady, setIsReady] = useState(false);
-  const { coordinator, initializeData } = useMosaicCoordinator();
-
-  useEffect(() => {
-    initializeData().then(() => setIsReady(true));
-  }, []);
-
-  return (
-    
-      {isReady ? (
-        

-          

-            
-          

-        

-    ) : (
-      

-        

-          Loading...
-        

-      

-    )}
-
-    
-  );
-};
\ No newline at end of file
diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx
index c3bb980a..704df8fb 100644
--- a/ui/src/pages/bed-splash.tsx
+++ b/ui/src/pages/bed-splash.tsx
@@ -17,8 +17,7 @@ import { snakeToTitleCase } from '../utils';
 import { Text2BedSearchResultsTable } from '../components/search/text2bed/t2b-search-results-table';
 import { useBedNeighbours } from '../queries/useBedNeighbours';
 import type { components } from '../../bedbase-types.d.ts';
-// import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx';
-import { BADAtlas } from '../components/bed-splash-components/bad-atlas.tsx';
+import { BEDEmbeddingView } from '../components/umap/bed-embedding-view.tsx';
 import { useState } from 'react';
 
 // Use the response type to properly type the metadata
@@ -277,8 +276,7 @@ export const BedSplash = () => {
 
           {bedId && metadata?.name?.includes('encode') && (
             <>
-              
-              {/*  */}
+              
             
           )}
 
diff --git a/ui/src/pages/bed-umap.tsx b/ui/src/pages/bed-umap.tsx
new file mode 100644
index 00000000..3544e2ea
--- /dev/null
+++ b/ui/src/pages/bed-umap.tsx
@@ -0,0 +1,16 @@
+// import { useSearchParams } from 'react-router-dom';
+import { Layout } from '../components/layout';
+import { BEDEmbeddingAtlas } from '../components/umap/bed-embedding-atlas';
+
+export const BEDUmap: React.FC = () => {
+  // const [searchParams] = useSearchParams();
+
+  // const bedId = searchParams.get('searchId');
+  // console.log(bedId);
+
+  return (
+    
+      
+    
+  );
+};

From 3730ad5ab22a028b56e47bcad9365b57394fa47b Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 11 Nov 2025 11:30:41 -0500
Subject: [PATCH 33/65] Added umap endpoint

---
 bedhost/routers/bed_api.py                 | 25 ++++++++++++++++++++++
 deployment/config/api-dev.bedbase.org.yaml |  1 +
 requirements/requirements-all.txt          |  4 ++--
 3 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/bedhost/routers/bed_api.py b/bedhost/routers/bed_api.py
index ce885a2d..96a889b3 100644
--- a/bedhost/routers/bed_api.py
+++ b/bedhost/routers/bed_api.py
@@ -261,6 +261,31 @@ async def embed_bed_file(
             embedding = bbagent.bed._embed_file(region_set)
     return embedding.tolist()[0]
 
+@router.post(
+    "/umap",
+    summary="Get embeddings for a bed file.",
+    response_model=List[float],
+)
+async def embed_bed_file(
+    file: UploadFile = File(None),
+):
+    """
+    Create embedding for bed file
+    """
+    _LOGGER.info("Embedding file..")
+
+    if file is not None:
+        with tempfile.TemporaryDirectory() as dirpath:
+            file_path = os.path.join(dirpath, file.filename)
+
+            with open(file_path, "wb") as bed_file:
+                shutil.copyfileobj(file.file, bed_file)
+
+            region_set = RegionSet(file_path)
+
+            embedding = bbagent.bed._get_umap_file(region_set)
+    return embedding.tolist()[0]
+
 
 @router.get(
     "/missing_plots",
diff --git a/deployment/config/api-dev.bedbase.org.yaml b/deployment/config/api-dev.bedbase.org.yaml
index f3bba70e..ab3ab944 100644
--- a/deployment/config/api-dev.bedbase.org.yaml
+++ b/deployment/config/api-dev.bedbase.org.yaml
@@ -4,6 +4,7 @@ path:
   # region2vec: databio/r2v-pretrained-for-search
   region2vec: databio/r2v-encode-hg38
   vec2vec: 'databio/v2v-sentencetransformers-encode'
+  umap_model: "https://github.com/databio/bedbase-loader/raw/refs/heads/master/umap/hg38_umap_umap_model.joblib"
 database:
   host: $POSTGRES_HOST
   port: 5432
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 580bd04f..cba08d95 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,5 +1,5 @@
-# bbconf @ git+https://github.com/databio/bbconf.git@comp_search#egg=bbconf
-bbconf>=0.12.0
+bbconf @ git+https://github.com/databio/bbconf.git@umap#egg=bbconf
+# bbconf>=0.12.0
 fastapi>=0.103.0
 logmuse>=0.2.7
 markdown

From 3d9367af5c12a8e0d73813955528edd666348632 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 11 Nov 2025 11:32:21 -0500
Subject: [PATCH 34/65] linting

---
 bedhost/routers/bed_api.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bedhost/routers/bed_api.py b/bedhost/routers/bed_api.py
index 96a889b3..5cbd9b5a 100644
--- a/bedhost/routers/bed_api.py
+++ b/bedhost/routers/bed_api.py
@@ -261,6 +261,7 @@ async def embed_bed_file(
             embedding = bbagent.bed._embed_file(region_set)
     return embedding.tolist()[0]
 
+
 @router.post(
     "/umap",
     summary="Get embeddings for a bed file.",

From 23e00a41d4854f7f8ed60b5a15fd9b6638a6fba1 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 11 Nov 2025 16:10:22 -0500
Subject: [PATCH 35/65] fixed test query parameter for multiple endpoints

---
 bedhost/helpers.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/bedhost/helpers.py b/bedhost/helpers.py
index eaf9b015..7d8e44d2 100644
--- a/bedhost/helpers.py
+++ b/bedhost/helpers.py
@@ -81,12 +81,10 @@ def drs_response(status_code, msg):
     return JSONResponse(status_code=status_code, content=content)
 
 
-test_query_parameter = (
-    Query(
-        False,
-        description="Internal parameter for testing purposes. If true, the request will not be counted.",
-        include_in_schema=False,
-    ),
+test_query_parameter = Query(
+    False,
+    description="Internal parameter for testing purposes. If true, the request will not be counted.",
+    include_in_schema=False,
 )
 
 

From 4faf3e6524e0f8dfbdca75f692f2b24b92cf71a6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 13 Nov 2025 22:33:37 +0000
Subject: [PATCH 36/65] Bump vega-interpreter from 2.0.0 to 2.2.1 in /ui

Bumps [vega-interpreter](https://github.com/vega/vega) from 2.0.0 to 2.2.1.
- [Release notes](https://github.com/vega/vega/releases)
- [Commits](https://github.com/vega/vega/compare/v2.0.0...v2.2.1)

---
updated-dependencies:
- dependency-name: vega-interpreter
  dependency-version: 2.2.1
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] 
---
 ui/package-lock.json | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 463ba7ef..e671fd54 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -5660,13 +5660,20 @@
       }
     },
     "node_modules/vega-interpreter": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/vega-interpreter/-/vega-interpreter-2.0.0.tgz",
-      "integrity": "sha512-ZjA7AC+xjfi4k9vgA49N5F/bS4fzf9E1KC0ljey4uMgHbmtKR53BWyOOzxHk+btfS9bEJ5gUvuoZzfqG3wIWEg==",
+      "version": "2.2.1",
+      "resolved": "https://registry.npmjs.org/vega-interpreter/-/vega-interpreter-2.2.1.tgz",
+      "integrity": "sha512-o+4ZEme2mdFLewlpF76dwPWW2VkZ3TAF3DMcq75/NzA5KPvnN4wnlCM8At2FVawbaHRyGdVkJSS5ROF5KwpHPQ==",
+      "license": "BSD-3-Clause",
       "dependencies": {
-        "vega-util": "^2.0.0"
+        "vega-util": "^2.1.0"
       }
     },
+    "node_modules/vega-interpreter/node_modules/vega-util": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/vega-util/-/vega-util-2.1.0.tgz",
+      "integrity": "sha512-PGfp0m0QCufDmcxKJCWQy4Ov23FoF8DSXmoJwSezi3itQaa2hbxK0+xwsTMP2vy4PR16Pu25HMzgMwXVW1+33w==",
+      "license": "BSD-3-Clause"
+    },
     "node_modules/vega-label": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/vega-label/-/vega-label-2.0.0.tgz",

From fa15ea282f9a1779d7ccb1fb47c4a67db9ca737b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 13 Nov 2025 22:33:50 +0000
Subject: [PATCH 37/65] Bump vega-expression, vega and vega-lite in /ui

Bumps [vega-expression](https://github.com/vega/vega), [vega](https://github.com/vega/vega) and [vega-lite](https://github.com/vega/vega-lite). These dependencies needed to be updated together.

Updates `vega-expression` from 6.0.0 to 6.1.0
- [Release notes](https://github.com/vega/vega/releases)
- [Commits](https://github.com/vega/vega/compare/v6.0.0...v6.1.0)

Updates `vega` from 6.1.2 to 6.2.0
- [Release notes](https://github.com/vega/vega/releases)
- [Commits](https://github.com/vega/vega/compare/v6.1.2...v6.2.0)

Updates `vega-lite` from 6.2.0 to 6.4.1
- [Release notes](https://github.com/vega/vega-lite/releases)
- [Changelog](https://github.com/vega/vega-lite/blob/main/CHANGELOG.md)
- [Commits](https://github.com/vega/vega-lite/compare/v6.2.0...v6.4.1)

---
updated-dependencies:
- dependency-name: vega-expression
  dependency-version: 6.1.0
  dependency-type: indirect
- dependency-name: vega
  dependency-version: 6.2.0
  dependency-type: indirect
- dependency-name: vega-lite
  dependency-version: 6.4.1
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] 
---
 ui/package-lock.json | 502 ++++++++++++++++++++-----------------------
 1 file changed, 232 insertions(+), 270 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 463ba7ef..d29c4db9 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -885,6 +885,7 @@
       "version": "7946.0.16",
       "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.16.tgz",
       "integrity": "sha512-6C8nqWur3j98U6+lXDfTUWIfgvZU+EumvpHKcYjujKH7woYyLj2sUmff0tRhrqM7BohUw7Pz3ZB1jj2gW9Fvmg==",
+      "license": "MIT",
       "peer": true
     },
     "node_modules/@types/hast": {
@@ -1676,6 +1677,7 @@
       "version": "7.2.0",
       "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
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-      "version": "6.0.0",
-      "resolved": "https://registry.npmjs.org/vega-view/-/vega-view-6.0.0.tgz",
-      "integrity": "sha512-Q4bS6eEt+d8N1ZKGg/jueEFboR1CGO8olye7vz3gS/iyg4fPDwMx0sh4pDiX077OPD3UW/0NbplIiHwzQyabEg==",
+      "version": "6.1.0",
+      "resolved": "https://registry.npmjs.org/vega-view/-/vega-view-6.1.0.tgz",
+      "integrity": "sha512-hmHDm/zC65lb23mb9Tr9Gx0wkxP0TMS31LpMPYxIZpvInxvUn7TYitkOtz1elr63k2YZrgmF7ztdGyQ4iCQ5fQ==",
+      "license": "BSD-3-Clause",
       "peer": true,
       "dependencies": {
         "d3-array": "^3.2.4",
         "d3-timer": "^3.0.1",
-        "vega-dataflow": "^6.0.0",
-        "vega-format": "^2.0.0",
-        "vega-functions": "^6.0.0",
-        "vega-runtime": "^7.0.0",
-        "vega-scenegraph": "^5.0.0",
-        "vega-util": "^2.0.0"
+        "vega-dataflow": "^6.1.0",
+        "vega-format": "^2.1.0",
+        "vega-functions": "^6.1.0",
+        "vega-runtime": "^7.1.0",
+        "vega-scenegraph": "^5.1.0",
+        "vega-util": "^2.1.0"
       }
     },
     "node_modules/vega-view-transforms": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/vega-view-transforms/-/vega-view-transforms-5.0.0.tgz",
-      "integrity": "sha512-AqQStHIYZtjsm84rx43z6P18DdR4/l20q/mfWXJ2Ifts1T2gPshC24/0xUfGrnwpqM5m3X1HwkJUiyEJxzVQrQ==",
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/vega-view-transforms/-/vega-view-transforms-5.1.0.tgz",
+      "integrity": "sha512-fpigh/xn/32t+An1ShoY3MLeGzNdlbAp2+HvFKzPpmpMTZqJEWkk/J/wHU7Swyc28Ta7W1z3fO+8dZkOYO5TWQ==",
+      "license": "BSD-3-Clause",
       "peer": true,
       "dependencies": {
-        "vega-dataflow": "^6.0.0",
-        "vega-scenegraph": "^5.0.0",
-        "vega-util": "^2.0.0"
+        "vega-dataflow": "^6.1.0",
+        "vega-scenegraph": "^5.1.0",
+        "vega-util": "^2.1.0"
       }
     },
     "node_modules/vega-voronoi": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/vega-voronoi/-/vega-voronoi-5.0.0.tgz",
-      "integrity": "sha512-mmsQFo7Aj8WM/QS8Ta79QWxADU3WpvEQ0OIR20WFgY/QLJ+42FEcJkBlaSQQ+DFl2Ci5PdbpZtRFMPJoRokFMw==",
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/vega-voronoi/-/vega-voronoi-5.1.0.tgz",
+      "integrity": "sha512-uKdsoR9x60mz7eYtVG+NhlkdQXeVdMr6jHNAHxs+W+i6kawkUp5S9jp1xf1FmW/uZvtO1eqinHQNwATcDRsiUg==",
+      "license": "BSD-3-Clause",
       "peer": true,
       "dependencies": {
         "d3-delaunay": "^6.0.4",
-        "vega-dataflow": "^6.0.0",
-        "vega-util": "^2.0.0"
+        "vega-dataflow": "^6.1.0",
+        "vega-util": "^2.1.0"
       }
     },
     "node_modules/vega-wordcloud": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/vega-wordcloud/-/vega-wordcloud-5.0.0.tgz",
-      "integrity": "sha512-Rm46D1ginGdunWLtsiymllU5RvJTEtpKRaWcc/pABpFiz7QHGGrZ9FhOczxW1o3n89h07gzc9n8xlWYco06Fdw==",
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/vega-wordcloud/-/vega-wordcloud-5.1.0.tgz",
+      "integrity": "sha512-sSdNmT8y2D7xXhM2h76dKyaYn3PA4eV49WUUkfYfqHz/vpcu10GSAoFxLhQQTkbZXR+q5ZB63tFUow9W2IFo6g==",
+      "license": "BSD-3-Clause",
       "peer": true,
       "dependencies": {
         "vega-canvas": "^2.0.0",
-        "vega-dataflow": "^6.0.0",
-        "vega-scale": "^8.0.0",
+        "vega-dataflow": "^6.1.0",
+        "vega-scale": "^8.1.0",
         "vega-statistics": "^2.0.0",
-        "vega-util": "^2.0.0"
+        "vega-util": "^2.1.0"
       }
     },
     "node_modules/vfile": {
@@ -6072,15 +6043,6 @@
         "loose-envify": "^1.0.0"
       }
     },
-    "node_modules/web-streams-polyfill": {
-      "version": "3.3.3",
-      "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.3.3.tgz",
-      "integrity": "sha512-d2JWLCivmZYTSIoge9MsgFCZrt571BikcWGYkjC1khllbTeDlGqZ2D8vD8E/lJa8WGWbb7Plm8/XJYV7IJHZZw==",
-      "peer": true,
-      "engines": {
-        "node": ">= 8"
-      }
-    },
     "node_modules/which": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",

From 995df0f62a27f4d8b4dd68e5222b971853129adf Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Thu, 13 Nov 2025 18:05:20 -0500
Subject: [PATCH 38/65] rudimentary bed umap upload functionality

---
 .../atlas-tooltip.tsx                         |  12 +-
 ui/src/components/umap/bed-embedding-view.tsx | 110 ++++++++++++++++--
 .../contexts/mosaic-coordinator-context.tsx   |  51 +++++++-
 ui/src/queries/useBedUmap.ts                  |  29 +++++
 ui/vite.config.ts                             |  10 ++
 5 files changed, 198 insertions(+), 14 deletions(-)
 rename ui/src/components/{bed-splash-components => umap}/atlas-tooltip.tsx (79%)
 create mode 100644 ui/src/queries/useBedUmap.ts

diff --git a/ui/src/components/bed-splash-components/atlas-tooltip.tsx b/ui/src/components/umap/atlas-tooltip.tsx
similarity index 79%
rename from ui/src/components/bed-splash-components/atlas-tooltip.tsx
rename to ui/src/components/umap/atlas-tooltip.tsx
index a9168114..0fa0e7a7 100644
--- a/ui/src/components/bed-splash-components/atlas-tooltip.tsx
+++ b/ui/src/components/umap/atlas-tooltip.tsx
@@ -9,13 +9,17 @@ interface TooltipProps {
       'Cell Line': string;
       Description: string;
     };
-    category?: string;
+    category?: number;
+    x?: number;
+    y?: number;
   };
 }
 
 const TooltipContent = ({ tooltip }: { tooltip: TooltipProps['tooltip'] }) => {
   if (!tooltip) return null;
 
+  console.log(tooltip)
+
   return (
     
 {
             
               id:{' '}{tooltip.identifier || 'N/A'}
             
+            
+              x:{' '}{tooltip.x ? tooltip.x.toFixed(6) : 'N/A'}
+            
+            
+              y:{' '}{tooltip.y ? tooltip.y.toFixed(6) : 'N/A'}
+            
           

         
       )}
diff --git a/ui/src/components/umap/bed-embedding-view.tsx b/ui/src/components/umap/bed-embedding-view.tsx
index 40ae689b..0cc2da44 100644
--- a/ui/src/components/umap/bed-embedding-view.tsx
+++ b/ui/src/components/umap/bed-embedding-view.tsx
@@ -5,8 +5,9 @@ import * as vg from '@uwdata/vgplot'
 import { isPointInPolygon, tableau20 } from '../../utils';
 import { useBedCart } from '../../contexts/bedcart-context';
 import { components } from '../../../bedbase-types';
-import { AtlasTooltip } from '../bed-splash-components/atlas-tooltip';
+import { AtlasTooltip } from './atlas-tooltip';
 import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context';
+import { useBedUmap } from '../../queries/useBedUmap';
 
 type SearchResponse = components['schemas']['BedListSearchResult'];
 
@@ -14,14 +15,19 @@ type Props = {
   bedId: string;
   neighbors?: SearchResponse;
   showNeighbors?: boolean;
+  enableUpload?: boolean;
 }
 
 export const BEDEmbeddingView = (props: Props) => {
   const { bedId, neighbors, showNeighbors } = props;
-  const { coordinator, initializeData } = useMosaicCoordinator();
+  const { coordinator, initializeData, addCustomPoint, deleteCustomPoint } = useMosaicCoordinator();
   const { addBedToCart } = useBedCart();
+  const { mutateAsync: getUmapCoordinates } = useBedUmap();
+
+  const enableUpload = true;
 
   const containerRef = useRef(null);
+  const fileInputRef = useRef(null);
 
   const [containerWidth, setContainerWidth] = useState(900);
   const [isReady, setIsReady] = useState(false);
@@ -33,6 +39,8 @@ export const BEDEmbeddingView = (props: Props) => {
   const [filterSelection, setFilterSelection] = useState(null);
   const [addedToCart, setAddedToCart] = useState(false);
   const [tooltipPoint, setTooltipPoint] = useState(null);
+  const [uploadedFilename, setUploadedFilename] = useState('');
+  const [dataVersion, setDataVersion] = useState(0);
 
   const filter = useMemo(() => vg.Selection.intersect(), []);
   const legendFilterSource = useMemo(() => ({}), []);
@@ -115,6 +123,47 @@ export const BEDEmbeddingView = (props: Props) => {
     setSelectedPoints(finalPoints);
   };
 
+  const handleFileRemove = async () => {
+    try {
+      await deleteCustomPoint();
+      setUploadedFilename('')
+
+      coordinator.clear();
+      const updatedLegend = await fetchLegendItems(coordinator);
+      setLegendItems(updatedLegend);
+      setDataVersion(v => v + 1);
+    } catch (error) {
+      console.error('Error deleting file');
+    }
+  }
+
+  const handleFileUpload = async (event: React.ChangeEvent) => {
+    const file = event.target.files?.[0];
+    if (!file) return;
+
+    try {
+      const coordinates = await getUmapCoordinates(file);
+
+      if (coordinates.length >= 2) {
+        await addCustomPoint(coordinates[0], coordinates[1]);
+        setUploadedFilename(file.name)
+
+        // Clear coordinator cache and refresh legend
+        coordinator.clear();
+        const updatedLegend = await fetchLegendItems(coordinator);
+        setLegendItems(updatedLegend);
+        setDataVersion(v => v + 1);
+        centerOnPoint({x: coordinates[0], y: coordinates[1]}, 0.3)
+      }
+    } catch (error) {
+      console.error('Error getting UMAP coordinates:', error);
+    }
+  };
+
+  const handleUploadClick = () => {
+    fileInputRef.current?.click();
+  };
+
   // Range selection (for rectangle/lasso)
   const handleRangeSelection = async (coordinator: any, value: any) => {
     // console.log('Range selection updated:', value);
@@ -212,14 +261,15 @@ export const BEDEmbeddingView = (props: Props) => {
   };
 
   const fetchLegendItems = async (coordinator: any) => {
-    const result = await coordinator.query(
-      `SELECT DISTINCT
+    const query = `SELECT DISTINCT
         ${colorGrouping.replace('_category', '')} as name,
         ${colorGrouping} as category
         FROM data
-        ORDER BY ${colorGrouping}`,
-      { type: 'json' }
-    ) as any[];
+        ORDER BY ${colorGrouping}`;
+
+    console.log('Legend query:', query);
+    const result = await coordinator.query(query, { type: 'json' }) as any[];
+    console.log('Legend results:', result);
 
     return result
   }
@@ -230,6 +280,11 @@ export const BEDEmbeddingView = (props: Props) => {
     });
   }, []);
 
+  // useEffect(() => { // add point
+  //   addPoint(20, 20).then(() => {
+  //   });
+  // }, []);
+
   useEffect(() => { // resize width of view
     if (containerRef.current) {
       setContainerWidth(containerRef.current.offsetWidth);
@@ -285,9 +340,41 @@ export const BEDEmbeddingView = (props: Props) => {
   return (
     <>
       

-        

-          
BED Embedding Atlas

-        

+        {
+          enableUpload ? (
+            

+              

+                
BED Embedding Atlas

+                
+                
+                {!!uploadedFilename && (
+                  
+                    {uploadedFilename}
+                    
+                  
+                )}
+              

+            

+          ) : (
+            

+              
BED Embedding Atlas

+            

+          )
+        }
       

       {isReady ? (
         

@@ -295,6 +382,7 @@ export const BEDEmbeddingView = (props: Props) => {
             

               

                  {
                   
                   
                     {getSortedSelectedPoints().map((point: any, index: number) => (
-                       centerOnPoint(point, 0.3)} key={index}>
+                       centerOnPoint(point, 0.3)} key={point.identifier + '_' + index}>
                         {point.text}
                         {point.fields.Assay}
                         {point.fields['Cell Line']}
diff --git a/ui/src/contexts/mosaic-coordinator-context.tsx b/ui/src/contexts/mosaic-coordinator-context.tsx
index 0da56cc1..8dc1879f 100644
--- a/ui/src/contexts/mosaic-coordinator-context.tsx
+++ b/ui/src/contexts/mosaic-coordinator-context.tsx
@@ -4,6 +4,8 @@ import * as vg from '@uwdata/vgplot';
 interface MosaicCoordinatorContextType {
   getCoordinator: () => vg.Coordinator;
   initializeData: () => Promise;
+  addCustomPoint: (x: number, y: number) => Promise;
+  deleteCustomPoint: () => Promise;
 }
 
 const MosaicCoordinatorContext = createContext(null);
@@ -43,7 +45,50 @@ export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode })
     dataInitializedRef.current = true;
   };
 
-  const value = useMemo(() => ({ getCoordinator, initializeData }), []);
+  const deleteCustomPoint = async () => {
+    const coordinator = getCoordinator();
+
+    await coordinator.exec([
+      vg.sql`DELETE FROM data WHERE id = 'custom_point'` as any
+    ]);
+  }
+
+  const addCustomPoint = async (x: number, y: number) => {
+    const coordinator = getCoordinator();
+
+    await coordinator.exec([
+      vg.sql`DELETE FROM data WHERE id = 'custom_point'` as any
+    ]);
+
+    // Get max category indices for uploaded points (after deletion to ensure clean state)
+    const maxCategories = await coordinator.query(
+      `SELECT
+        MAX(assay_category) as max_assay_category,
+        MAX(cell_line_category) as max_cell_line_category
+       FROM data`,
+      { type: 'json' }
+    ) as any[];
+
+    const assayCategory = (maxCategories[0]?.max_assay_category ?? -1) + 1;
+    const cellLineCategory = (maxCategories[0]?.max_cell_line_category ?? -1) + 1;
+
+    await coordinator.exec([
+      vg.sql`INSERT INTO data VALUES (
+        ${x},
+        ${y},
+        0,
+        'custom_point',
+        'Your uploaded file',
+        'User uploaded BED file',
+        'Uploaded BED',
+        'Uploaded BED',
+        ${assayCategory},
+        ${cellLineCategory}
+      )` as any,
+    ]);
+  };
+
+  const value = useMemo(() => ({ getCoordinator, initializeData, addCustomPoint, deleteCustomPoint }), []);
   return (
     
       {children}
@@ -58,7 +103,9 @@ export const useMosaicCoordinator = () => {
   }
   return {
     coordinator: context.getCoordinator(),
-    initializeData: context.initializeData
+    initializeData: context.initializeData,
+    addCustomPoint: context.addCustomPoint,
+    deleteCustomPoint: context.deleteCustomPoint
   };
 };
 
diff --git a/ui/src/queries/useBedUmap.ts b/ui/src/queries/useBedUmap.ts
new file mode 100644
index 00000000..6d9c8ed1
--- /dev/null
+++ b/ui/src/queries/useBedUmap.ts
@@ -0,0 +1,29 @@
+import { useMutation, useQueryClient } from '@tanstack/react-query';
+import { AxiosInstance } from 'axios';
+import { useBedbaseApi } from '../contexts/api-context';
+
+type UmapResponse = number[];
+
+const getBedUmap = async (file: File, axiosInstance: AxiosInstance) => {
+  const formData = new FormData();
+  formData.append('file', file);
+
+  const { data } = await axiosInstance.post('/bed/umap', formData, {
+    headers: {
+      'Content-Type': 'multipart/form-data',
+    },
+  });
+  return data;
+};
+
+export const useBedUmap = () => {
+  const queryClient = useQueryClient();
+  const { api } = useBedbaseApi();
+
+  return useMutation({
+    mutationFn: (file: File) => getBedUmap(file, api),
+    onSuccess: () => {
+      queryClient.invalidateQueries({ queryKey: ['bed-umap'] });
+    },
+  });
+};
diff --git a/ui/vite.config.ts b/ui/vite.config.ts
index 5a33944a..3b1a7fee 100644
--- a/ui/vite.config.ts
+++ b/ui/vite.config.ts
@@ -4,4 +4,14 @@ import react from '@vitejs/plugin-react'
 // https://vitejs.dev/config/
 export default defineConfig({
   plugins: [react()],
+  server: {
+    proxy: {
+      '/api': {
+        target: 'https://api-dev.bedbase.org/v1',
+        changeOrigin: true,
+        rewrite: (path) => path.replace(/^\/api/, ''),
+        secure: false,
+      }
+    }
+  }
 })

From a86037fa97966e2b1f7b880f24db52827b2ede54 Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Fri, 14 Nov 2025 12:44:04 -0500
Subject: [PATCH 39/65] highlight uploaded bed file on umap

---
 ui/src/components/umap/bed-embedding-view.tsx | 152 +++++++++++-------
 ui/src/pages/bed-splash.tsx                   |   2 +-
 2 files changed, 99 insertions(+), 55 deletions(-)

diff --git a/ui/src/components/umap/bed-embedding-view.tsx b/ui/src/components/umap/bed-embedding-view.tsx
index 0cc2da44..f0c76c64 100644
--- a/ui/src/components/umap/bed-embedding-view.tsx
+++ b/ui/src/components/umap/bed-embedding-view.tsx
@@ -19,13 +19,11 @@ type Props = {
 }
 
 export const BEDEmbeddingView = (props: Props) => {
-  const { bedId, neighbors, showNeighbors } = props;
+  const { bedId, neighbors, showNeighbors, enableUpload } = props;
   const { coordinator, initializeData, addCustomPoint, deleteCustomPoint } = useMosaicCoordinator();
   const { addBedToCart } = useBedCart();
   const { mutateAsync: getUmapCoordinates } = useBedUmap();
 
-  const enableUpload = true;
-
   const containerRef = useRef(null);
   const fileInputRef = useRef(null);
 
@@ -41,6 +39,7 @@ export const BEDEmbeddingView = (props: Props) => {
   const [tooltipPoint, setTooltipPoint] = useState(null);
   const [uploadedFilename, setUploadedFilename] = useState('');
   const [dataVersion, setDataVersion] = useState(0);
+  const [pendingSelection, setPendingSelection] = useState(null);
 
   const filter = useMemo(() => vg.Selection.intersect(), []);
   const legendFilterSource = useMemo(() => ({}), []);
@@ -55,6 +54,82 @@ export const BEDEmbeddingView = (props: Props) => {
     });
   };
 
+  const handleFileRemove = async () => {
+    try {
+      await deleteCustomPoint();
+      setUploadedFilename('')
+
+      coordinator.clear();
+      const updatedLegend = await fetchLegendItems(coordinator);
+      setLegendItems(updatedLegend);
+
+      // Prepare selection without custom point
+      const newSelection = selectedPoints.filter((p: any) => p.identifier !== 'custom_point');
+      setPendingSelection(newSelection);
+
+      // Force remount to remove point from map
+      setDataVersion(v => v + 1);
+    } catch (error) {
+      console.error('Error deleting file');
+    }
+  }
+
+  const handleFileUpload = async (event: React.ChangeEvent) => {
+    const file = event.target.files?.[0];
+    if (!file) return;
+
+    try {
+      const coordinates = await getUmapCoordinates(file);
+
+      if (coordinates.length >= 2) {
+        await addCustomPoint(coordinates[0], coordinates[1]);
+        setUploadedFilename(file.name)
+
+        // Clear coordinator cache and refresh legend
+        coordinator.clear();
+        const updatedLegend = await fetchLegendItems(coordinator);
+        setLegendItems(updatedLegend);
+
+        // await new Promise(resolve => setTimeout(resolve, 150));
+
+        // Query the uploaded point
+        const customPoint: any = await coordinator.query(
+          `SELECT
+            x, y,
+            ${colorGrouping} as category,
+            name as text,
+            id as identifier,
+            {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields
+            FROM data
+            WHERE id = 'custom_point'`,
+          { type: 'json' }
+        );
+
+        if (customPoint && customPoint.length > 0) {
+          // console.log('Custom point queried:', customPoint[0]);
+
+          // Prepare selection to apply after remount
+          const newSelection = selectedPoints.filter((p: any) => p.identifier !== 'custom_point');
+          newSelection.push(customPoint[0]);
+          setPendingSelection(newSelection);          
+
+          // Force remount to show new point
+          setDataVersion(v => v + 1);
+        }
+      }
+    } catch (error) {
+      console.error('Error getting UMAP coordinates:', error);
+    } finally {
+      if (fileInputRef.current) {
+        fileInputRef.current.value = '';
+      }
+    }
+  };
+
+  const handleUploadClick = () => {
+    fileInputRef.current?.click();
+  };
+
   const getSortedSelectedPoints = () => {
     if (!selectedPoints || selectedPoints.length === 0) return [];
 
@@ -123,47 +198,6 @@ export const BEDEmbeddingView = (props: Props) => {
     setSelectedPoints(finalPoints);
   };
 
-  const handleFileRemove = async () => {
-    try {
-      await deleteCustomPoint();
-      setUploadedFilename('')
-
-      coordinator.clear();
-      const updatedLegend = await fetchLegendItems(coordinator);
-      setLegendItems(updatedLegend);
-      setDataVersion(v => v + 1);
-    } catch (error) {
-      console.error('Error deleting file');
-    }
-  }
-
-  const handleFileUpload = async (event: React.ChangeEvent) => {
-    const file = event.target.files?.[0];
-    if (!file) return;
-
-    try {
-      const coordinates = await getUmapCoordinates(file);
-
-      if (coordinates.length >= 2) {
-        await addCustomPoint(coordinates[0], coordinates[1]);
-        setUploadedFilename(file.name)
-
-        // Clear coordinator cache and refresh legend
-        coordinator.clear();
-        const updatedLegend = await fetchLegendItems(coordinator);
-        setLegendItems(updatedLegend);
-        setDataVersion(v => v + 1);
-        centerOnPoint({x: coordinates[0], y: coordinates[1]}, 0.3)
-      }
-    } catch (error) {
-      console.error('Error getting UMAP coordinates:', error);
-    }
-  };
-
-  const handleUploadClick = () => {
-    fileInputRef.current?.click();
-  };
-
   // Range selection (for rectangle/lasso)
   const handleRangeSelection = async (coordinator: any, value: any) => {
     // console.log('Range selection updated:', value);
@@ -267,10 +301,7 @@ export const BEDEmbeddingView = (props: Props) => {
         FROM data
         ORDER BY ${colorGrouping}`;
 
-    console.log('Legend query:', query);
     const result = await coordinator.query(query, { type: 'json' }) as any[];
-    console.log('Legend results:', result);
-
     return result
   }
 
@@ -280,11 +311,6 @@ export const BEDEmbeddingView = (props: Props) => {
     });
   }, []);
 
-  // useEffect(() => { // add point
-  //   addPoint(20, 20).then(() => {
-  //   });
-  // }, []);
-
   useEffect(() => { // resize width of view
     if (containerRef.current) {
       setContainerWidth(containerRef.current.offsetWidth);
@@ -299,6 +325,22 @@ export const BEDEmbeddingView = (props: Props) => {
     }
   }, [isReady, colorGrouping])
 
+  useEffect(() => { // apply pending selection after dataVersion change
+    if (pendingSelection !== null) {
+      setTimeout(() => {
+        setSelectedPoints(pendingSelection);
+        // If there's an uploaded file, center on it and set tooltip
+        if (uploadedFilename) {
+          const uploadedPoint = pendingSelection.find((point: any) => point.identifier === 'custom_point');
+          if (uploadedPoint) {
+            centerOnPoint(uploadedPoint, 0.3);
+          }
+        }
+        setPendingSelection(null);
+      }, 200);
+    }
+  }, [dataVersion, pendingSelection])
+
   useEffect(() => { // fetch initial bed id and neighbors
     if (isReady) {
       setTimeout(async () => {
@@ -330,6 +372,8 @@ export const BEDEmbeddingView = (props: Props) => {
             { type: 'json' }
           );
           setSelectedPoints([currentBed[0], ...neighborPoints]);
+        } else if (showNeighbors && enableUpload) {
+          setSelectedPoints([currentBed[0]]);
         } else {
           setSelectedPoints([currentBed[0]]);
         }
@@ -355,7 +399,7 @@ export const BEDEmbeddingView = (props: Props) => {
                   ref={fileInputRef}
                   className="d-none"
                   type="file"
-                  accept=".bed,.bed.gz"
+                  accept=".bed,.gz,application/gzip,application/x-gzip"
                   onChange={handleFileUpload}
                 />
                 {!!uploadedFilename && (
@@ -484,7 +528,7 @@ export const BEDEmbeddingView = (props: Props) => {
                 {/*  */}
                  */}
+          

           
         

-        

-          {/*Or, explore an example BED file*/}
-          Or, explore an example BED file
-          or an{' '} example BEDset
-        

 
-        

-          
-          
-          

-            

-              BEDbase logo
-            

+        {searchOptions && (
+          

+            test
           

-          
-          

-            

-              
Statistics

-              

-                Statistics icon
-              

-            

-            

-              
BED sets

-              

-                Statistics icon
-              

-            

-            

-              
Embeddings

-              

-                Statistics icon
+        )}
+
+        

+          
+        

+        

+          explore the BED file embedding space above, or visit a random BED file
+          or  BEDset
+        

+
+        

+          
+            {(bedbaseStats?.bedfiles_number || '-').toLocaleString()} BED files
+          
+          •
+          
+            {(bedbaseStats?.bedsets_number || '-').toLocaleString()} BEDsets
+          
+          •
+          
+            {(bedbaseStats?.genomes_number || '-').toLocaleString()} genomes
+          
+          •
+          
+            more metrics
+            
+          
+        

+
+        

+          

+            

+              

+                

+                  

+                    

+                      
+                      
Vector Search

+                    

+                    

+                      Search by text, upload BED files for similarity matching, or browse BEDsets. Explore results directly within their region embedding space.
+                    

+                    
+                    
+                  

+                

+
+                

+                  

+                    

+                      
+                      
BED Analyzer

+                    

+                    

+                      Analyze any BED file in your browser with our gtars-wasm integration. Get file statistics, region distributions, and chromosome coverage instantly.
+                    

+                    
+                      BED Analyzer
+                    
+                  

+                

               

             

-          

-        

-        

-          
-            
-              
Web Server and API

-              

-                The BEDbase web server and API are designed to provide a user-friendly interface for exploring and
-                working with genomic region data. The web server allows users to search for BED files and BED sets, view
-                detailed information about specific files, and create collections of files.
-              

-            
-            
-              

-                
-                  

-                    
+                    
                   

-                  
+                  

                     {CODE_SNIPPETS.map((snippet) => (
-                      
-                        
+                      

+                        
                           {snippet.code}
                         
-                        

-                          
-                        

-                      
+                      

                     ))}
-                  
-                
-              

-            
-          
-          
-            
-              
BED Embedding Visualization

-              

-                BEDbase supports visualization of UMAP of hg38 BED embeddings. It allows users to explore the
-                similarity of genomic regions based on their embeddings, and
-                providing insights into the relationships between different BED files.
-                The visualization is available on the UMAP visualization.
-              

-            
-            
-              UMAP visualization
-            
-          
-          
-            
-              
Search for BED Files

-              

-                BEDbase offers three search endpoints for discovering BED files and BEDsets, distinguishing itself from
-                other platforms by utilizing vector search to index and search through bed file regions. This approach
-                enhances search accuracy and efficiency compared to platforms relying on unstructured user-provided
-                metadata, which can be ambiguous and less reliable. User can search for BED files by providing a query
-                string, or a BED file.
-              

-            
-            
-              

-                 setSearchTermSmall(e.target.value)}
-                  onKeyDown={(e) => {
-                    if (e.key === 'Enter') {
-                      if (searchTermSmall.length === 0) {
-                        return;
-                      }
-                      navigate(`/search?q=${searchTermSmall}`);
-                    }
-                  }}
-                  className="p-2 rounded border w-100 shadow-sm"
-                />
-                
+                  

+                  

+                    
+                  

+                

+                

+                  

+                    
+                    
REST API

+                  

+                  

+                    Programmatic access to the BEDbase web server with a RESTful API. Query, retrieve, and analyze genomic regions with simple HTTP requests from any language.
+                  

+                  
+                    API Docs
+                  
+                

               

-            
-          
-          {/* 
 */}
-          
-            
-              
BEDbase Client 

-              

-                BEDbase provides a Python an R client for interacting with the BEDbase API. The client allows users to
-                download, cache, and analyze BED files and BED sets programmatically, without the need to interact with
-                the native API. BBclient is available on PyPI in geniml package with other useful tools for genomic data
-                analysis. Python Geniml package:{' '}
-                
-                  {' '}
-                  PyPI geniml
-                
-                .
-                R package:{' '}
-                
-                  {' '}
-                  BEDbaser
-                
-                .
-              

-            
+            

 
-            
-              

-                
-                  

-                    
+                    
                   

-                  
+                  

                     {BBCONF_SNIPPETS.map((snippet) => (
-                      
-                        
+                      

+                        
                           {snippet.code}
                         
-                        

-                          
-                        

-                      
+                      

                     ))}
-                  
-                
-              

-            
-          
-          
-            
-              
Data Availability Summary

-              

-                Comprehensive metrics about BEDbase file statistics is available on the {' '}
-                metrics page.
-              

-            
-            
-              

-                
    
-                  
  • 
-                    Number of bed files available:
-                    {(bedbaseStats?.bedfiles_number || 0).toLocaleString()}
-                  
    • 
-                  
  • 
-                    Number of bed sets available:
-                    {(bedbaseStats?.bedsets_number || 0).toLocaleString()}
-                  
    • 
-                  
  • 
-                    Number of genomes available:
-                    {(bedbaseStats?.genomes_number || 0).toLocaleString()}
-                  
    • 
-                

+                  

+                  

+                    
+                  

+                

+                

+                  

+                    
+                    
BEDbase Clients

+                  

+                  

+                    Download, cache, and analyze BED files programmatically with native Python and R packages. Simplifies API interaction through high-level interfaces.
+                  

+                  
+                

               

-            
-          
+            

+
+          

         

       

     

From 1a201b8981e89200cbc44a89f7daccc289cd4ccd Mon Sep 17 00:00:00 2001
From: Sam Park 
Date: Sat, 15 Nov 2025 00:56:25 -0500
Subject: [PATCH 45/65] color adjustment

---
 ui/src/components/layout.tsx                  | 18 ++++++++++--------
 ui/src/components/nav/nav.tsx                 |  3 +--
 ui/src/components/umap/bed-embedding-plot.tsx |  2 +-
 ui/src/custom.scss                            |  4 ++++
 ui/src/pages/home.tsx                         | 12 ++++++------
 5 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/ui/src/components/layout.tsx b/ui/src/components/layout.tsx
index df2db937..59e3529c 100644
--- a/ui/src/components/layout.tsx
+++ b/ui/src/components/layout.tsx
@@ -18,7 +18,7 @@ type LayoutProps = {
 const Footer = () => {
   const { data, isLoading, isFetching } = useServiceInfo();
   return (
-    

+
//
+
Region Distribution Plot
)} diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index 79c5f6fc..5cfc97a2 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -28,9 +28,7 @@ export const Home = () => { const handleSearch = () => { if (!searchTerm) { - toast.error('Please enter a search term.', { - position: 'top-center', - }); + toast.error('Please enter a search term.'); return; } navigate(`/search?q=${searchTerm}&view=${searchType}`); From 4eeebaea7ff7f56886cc5c4764585a3871eb823f Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 21 Nov 2025 19:31:21 -0500 Subject: [PATCH 63/65] minor detail --- .../bed-analytics-components/chromosome-stats-panel.tsx | 2 +- ui/src/components/umap/bed-embedding-atlas.tsx | 6 +++--- ui/src/contexts/mosaic-coordinator-context.tsx | 2 +- ui/src/pages/bed-analytics.tsx | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx index 380e7ce1..49046ecf 100644 --- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx +++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx @@ -53,7 +53,7 @@ const ChromosomeStatsPanel = ({ rs, selectedFile }: Props) => {
Number of regions per chromosome:
-
+
{containerWidth > 0 && }
diff --git a/ui/src/components/umap/bed-embedding-atlas.tsx b/ui/src/components/umap/bed-embedding-atlas.tsx index 93eb1e7e..4e020751 100644 --- a/ui/src/components/umap/bed-embedding-atlas.tsx +++ b/ui/src/components/umap/bed-embedding-atlas.tsx @@ -68,9 +68,9 @@ export const BEDEmbeddingAtlas = (props: Props) => { autoLabelEnabled: false, }} onStateChange={(e) => console.log(e)} - onExportSelection={async (predicate, format) => { - console.log('Export selection:', predicate, format); - }} + // onExportSelection={async (predicate, format) => { + // console.log('Export selection:', predicate, format); + // }} />
diff --git a/ui/src/contexts/mosaic-coordinator-context.tsx b/ui/src/contexts/mosaic-coordinator-context.tsx index 78859eb8..75ac8d03 100644 --- a/ui/src/contexts/mosaic-coordinator-context.tsx +++ b/ui/src/contexts/mosaic-coordinator-context.tsx @@ -117,7 +117,7 @@ export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode }) // Force WebGL by hiding WebGPU if not available if (!webgpuAvailable && webgl2Available) { - console.log('WebGPU not available, forcing WebGL2 fallback'); + // console.log('WebGPU not available, forcing WebGL2 fallback'); if ('gpu' in navigator) { Object.defineProperty(navigator, 'gpu', { get: () => undefined, diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 816e080a..af573f83 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -38,7 +38,7 @@ export const BEDAnalytics = () => { url.length === 32 && !url.startsWith('http') ? `https://api.bedbase.org/v1/files/files/${url[0]}/${url[1]}/${url}.bed.gz` : url; - console.log(`${fetchUrl}`); + // console.log(`${fetchUrl}`); const response = await fetch(fetchUrl); if (!response.ok) { throw new Error(`Failed to fetch BED file: ${response.statusText}`); From 150d90f572f3f8c2f8112070db4bf08be828b457 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 21 Nov 2025 22:39:18 -0500 Subject: [PATCH 64/65] index theme color --- ui/index.html | 1 + 1 file changed, 1 insertion(+) diff --git a/ui/index.html b/ui/index.html index 9b287e94..2a71bfb3 100644 --- a/ui/index.html +++ b/ui/index.html @@ -4,6 +4,7 @@ + BEDbase.org From 55995c0e1d26cd2af58fcf160d6f43df75ec150f Mon Sep 17 00:00:00 2001 From: Sam Park Date: Sat, 22 Nov 2025 13:52:26 -0500 Subject: [PATCH 65/65] spacing details --- ui/src/components/bed-splash-components/header.tsx | 12 ++++++------ .../bedset-splash-components/beds-table.tsx | 10 +++++----- .../components/bedset-splash-components/header.tsx | 10 +++++----- ui/src/components/nav/nav-desktop.tsx | 12 ++++++------ ui/src/components/nav/nav-logo.tsx | 2 +- 5 files changed, 23 insertions(+), 23 deletions(-) diff --git a/ui/src/components/bed-splash-components/header.tsx b/ui/src/components/bed-splash-components/header.tsx index 1511e2eb..affe23d5 100644 --- a/ui/src/components/bed-splash-components/header.tsx +++ b/ui/src/components/bed-splash-components/header.tsx @@ -65,30 +65,30 @@ export const BedSplashHeader = (props: Props) => {

)} -
+
{metadata?.processed && metadata?.genome_alias == 'hg38' && ( - )} - - {!addedToCart && cart[record_identifier || ''] ? (