simplify code

Author: LucaMarconato

CHANGELOG.md

@@ -12,167 +12,167 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
-- Transformations of Points and Shapes are now applied before rendering with datashader (#378)
-- Fix bug due to `sc.get.obs_df()` returning a different type (#393)
+-   Transformations of Points and Shapes are now applied before rendering with datashader (#378)
+-   Fix bug due to `sc.get.obs_df()` returning a different type (#393)
 
 ## [0.2.8] - 2024-11-26
 
 ### Changed
 
-- Support for `xarray.DataTree` (which moved from `datatree.DataTree`) (#380)
+-   Support for `xarray.DataTree` (which moved from `datatree.DataTree`) (#380)
 
 ## [0.2.7] - 2024-10-24
 
 ### Added
 
-- The user can now specify `datashader_reduction` to control the rendering behaviour (#309)
-- Rendering outlines of shapes with datashader works now (#309)
+-   The user can now specify `datashader_reduction` to control the rendering behaviour (#309)
+-   Rendering outlines of shapes with datashader works now (#309)
 
 ### Fixed
 
-- datashader now uses canvas size = image size which speeds up the rendering (#309)
-- datashader now uses the `linear` as interpolation method for colormaps instead of the default `eq_hist` to make it equivalent to matplotlib (#309)
-- point sizes of datashader now agree with matplotlib also when dpi != 100 (#309)
-- Giving a custom colormap when rendering a multiscale image now works (#586)
+-   datashader now uses canvas size = image size which speeds up the rendering (#309)
+-   datashader now uses the `linear` as interpolation method for colormaps instead of the default `eq_hist` to make it equivalent to matplotlib (#309)
+-   point sizes of datashader now agree with matplotlib also when dpi != 100 (#309)
+-   Giving a custom colormap when rendering a multiscale image now works (#586)
 
 ## [0.2.6] - 2024-09-04
 
 ### Changed
 
-- Lowered RMSE-threshold for plot-based tests from 45 to 15 (#344)
-- When subsetting to `groups`, `NA` isn't automatically added to legend (#344)
-- When rendering a single image channel, a colorbar is now shown (#346)
-- Removed `percentiles_for_norm` parameter (#346)
-- Changed `norm` to no longer accept bools, only `mpl.colors.Normalise` or `None` (#346)
+-   Lowered RMSE-threshold for plot-based tests from 45 to 15 (#344)
+-   When subsetting to `groups`, `NA` isn't automatically added to legend (#344)
+-   When rendering a single image channel, a colorbar is now shown (#346)
+-   Removed `percentiles_for_norm` parameter (#346)
+-   Changed `norm` to no longer accept bools, only `mpl.colors.Normalise` or `None` (#346)
 
 ### Fixed
 
-- Filtering with `groups` now preserves original cmap (#344)
-- Non-selected `groups` are now not shown in `na_color` (#344)
-- Several issues associated with `norm` and `colorbar` (#346)
+-   Filtering with `groups` now preserves original cmap (#344)
+-   Non-selected `groups` are now not shown in `na_color` (#344)
+-   Several issues associated with `norm` and `colorbar` (#346)
 
 ## [0.2.5] - 2024-08-23
 
 ### Changed
 
-- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
-- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
-- Removed `preprocessing` (.pp) accessor (#329)
+-   Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+-   Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+-   Removed `preprocessing` (.pp) accessor (#329)
 
 ### Fixed
 
-- Minor fixes for several tests as a result of the threshold change (#323)
+-   Minor fixes for several tests as a result of the threshold change (#323)
 
 ## [0.2.4] - 2024-08-07
 
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+-   Added utils function for 0-transparent cmaps (#302)
 
 ### Fixed
 
-- Took RNG out of categorical label test (#306)
-- Performance bug when plotting shapes (#298)
-- scale parameter was ignored for single-scale images (#301)
-- Changes to support for dask-expr (#283)
-- Added error handling for non-existent elements (#305)
-- Specifying vmin and vmax properly clips image data (#307)
-- import bug `get_cmap()` (8fd969c)
+-   Took RNG out of categorical label test (#306)
+-   Performance bug when plotting shapes (#298)
+-   scale parameter was ignored for single-scale images (#301)
+-   Changes to support for dask-expr (#283)
+-   Added error handling for non-existent elements (#305)
+-   Specifying vmin and vmax properly clips image data (#307)
+-   import bug `get_cmap()` (8fd969c)
 
 ## [0.2.3] - 2024-07-03
 
 ### Added
 
-- Datashader support for points and shapes (#244)
+-   Datashader support for points and shapes (#244)
 
 ### Changed
 
-- All parameters are now provided for a single element (#272)
+-   All parameters are now provided for a single element (#272)
 
 ### Fixed
 
-- Fix color assignment for NaN values (#257)
-- Zorder of rendering now strictly follows the order of the render_x calls (#244)
+-   Fix color assignment for NaN values (#257)
+-   Zorder of rendering now strictly follows the order of the render_x calls (#244)
 
 ## [0.2.2] - 2024-05-02
 
 ### Fixed
 
-- Fixed `fill_alpha` ignoring `alpha` channel from custom cmap (#236)
-- Fix channel str support (#221)
+-   Fixed `fill_alpha` ignoring `alpha` channel from custom cmap (#236)
+-   Fix channel str support (#221)
 
 ## [0.2.1] - 2024-03-26
 
 ### Minor
 
-- Adjusted GitHub worklows
+-   Adjusted GitHub worklows
 
 ## [0.2.0] - 2024-03-24
 
 ### Added
 
-- Support for plotting multiple tables @melonora
+-   Support for plotting multiple tables @melonora
 
 ### Fixed
 
-- Several bugfixes, especially for colors and palettes @melonora
+-   Several bugfixes, especially for colors and palettes @melonora
 
 ## [0.1.0] - 2024-01-17
 
 ### Added
 
-- Multiscale image handling: user can specify a scale, else the best scale is selected automatically given the figure size and dpi (#164)
-- Large images are automatically rasterized to speed up performance (#164)
-- Added better error message for mismatch in cs and ax number (#185)
-- Beter test coverage for correct plotting of elements after transformation (#198)
-- Can now stack render commands (#190, #192)
-- The `color` argument in render_shapes/points now accepts actual colors as well (#199)
-- Input arguments are now evaulated for their types in basic.py (#199)
+-   Multiscale image handling: user can specify a scale, else the best scale is selected automatically given the figure size and dpi (#164)
+-   Large images are automatically rasterized to speed up performance (#164)
+-   Added better error message for mismatch in cs and ax number (#185)
+-   Beter test coverage for correct plotting of elements after transformation (#198)
+-   Can now stack render commands (#190, #192)
+-   The `color` argument in render_shapes/points now accepts actual colors as well (#199)
+-   Input arguments are now evaulated for their types in basic.py (#199)
 
 ### Fixed
 
-- Now dropping index when plotting shapes after spatial query (#177)
-- Points are now being correctly rotated (#198)
-- User can now pass Colormap objects to the cmap argument in render_images. When only one cmap is given for 3 channels, it is now applied to each channel (#188, #194)
+-   Now dropping index when plotting shapes after spatial query (#177)
+-   Points are now being correctly rotated (#198)
+-   User can now pass Colormap objects to the cmap argument in render_images. When only one cmap is given for 3 channels, it is now applied to each channel (#188, #194)
 
 ## [0.0.6] - 2023-11-06
 
 ### Added
 
-- Pushed `get_extent` functionality upstream to `spatialdata` (#162)
+-   Pushed `get_extent` functionality upstream to `spatialdata` (#162)
 
 ## [0.0.5] - 2023-10-02
 
 ### Added
 
-- Can now scale shapes (#152)
-- Can now plot columns from GeoDataFrame (#149)
+-   Can now scale shapes (#152)
+-   Can now plot columns from GeoDataFrame (#149)
 
 ### Fixed
 
-- Multipolygons are now handled correctly (#93)
-- Legend order is now deterministic (#143)
-- Images no longer normalised by default (#150)
-- Filtering of shapes and points using the `groups` argument is now possible, coloring by palette and cmap arguments works for shapes and points (#153)
-- Colorbar no longer autoscales to [0, 1] (#155)
-- Plotting shapes after a spatial query is now possible (#163)
+-   Multipolygons are now handled correctly (#93)
+-   Legend order is now deterministic (#143)
+-   Images no longer normalised by default (#150)
+-   Filtering of shapes and points using the `groups` argument is now possible, coloring by palette and cmap arguments works for shapes and points (#153)
+-   Colorbar no longer autoscales to [0, 1] (#155)
+-   Plotting shapes after a spatial query is now possible (#163)
 
 ## [0.0.4] - 2023-08-11
 
 ### Fixed
 
-- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
-- Empty geometries among the shapes can be handeled (#133).
-- `outline_width` parameter in render_shapes is now a float that actually determines the line width (#139).
+-   Multi-scale images/labels are now correctly substituted and the action is logged (#131).
+-   Empty geometries among the shapes can be handeled (#133).
+-   `outline_width` parameter in render_shapes is now a float that actually determines the line width (#139).
 
 ## [0.0.2] - 2023-06-25
 
 ### Fixed
 
-- Multiple bugfixes of which I didn't keep track of.
+-   Multiple bugfixes of which I didn't keep track of.
 
 ## [0.0.1] - 2023-04-04
 
 ### Added
 
-- Initial release of `spatialdata-plot` with support for `images`, `labels`, `points` and `shapes`.
+-   Initial release of `spatialdata-plot` with support for `images`, `labels`, `points` and `shapes`.

README.md

@@ -26,8 +26,8 @@ SpatialData’s plotting capabilities allow to quickly visualise all contained m
 
 For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the
 
-- [API documentation][link-api].
-- [Example notebooks][link-notebooks] (section "Visiualizations")
+-   [API documentation][link-api].
+-   [Example notebooks][link-notebooks] (section "Visiualizations")
 
 ## Installation
 

docs/contributing.md

@@ -99,11 +99,11 @@ Specify `vX.X.X` as a tag name and create a release. For more information, see [
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
 
-- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
-- [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
-- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
-- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
-- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+-   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+-   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
+-   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+-   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+-   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
@@ -120,10 +120,10 @@ repository.
 
 #### Hints
 
-- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-  if you do so can sphinx automatically create a link to the external documentation.
-- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-  the `nitpick_ignore` list in `docs/conf.py`
+-   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+    if you do so can sphinx automatically create a link to the external documentation.
+-   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+    the `nitpick_ignore` list in `docs/conf.py`
 
 #### Building the docs locally
 

src/spatialdata_plot/pl/basic.py

@@ -950,10 +950,9 @@ def show(
 
                     if wanted_labels_on_this_cs:
                         if (table := params_copy.table_name) is not None:
-                            keys = [params_copy.color] if not isinstance(params_copy.color, list) else params_copy.color
-                            assert len(keys) == 1
-                            colors = sc.get.obs_df(sdata[table], keys)
-                            if isinstance(colors[keys[0]].dtype, pd.CategoricalDtype):
+                            assert isinstance(params_copy.color, str)
+                            colors = sc.get.obs_df(sdata[table], [params_copy.color])
+                            if isinstance(colors[params_copy.color].dtype, pd.CategoricalDtype):
                                 _maybe_set_colors(
                                     source=sdata[table],
                                     target=sdata[table],

src/spatialdata_plot/pl/render.py

@@ -453,11 +453,10 @@ def _render_points(
     )
 
     if col_for_color is not None:
-        keys = [col_for_color] if not isinstance(col_for_color, list) else col_for_color
-        assert len(keys) == 1
-        cols = sc.get.obs_df(adata, keys)
+        assert isinstance(col_for_color, str)
+        cols = sc.get.obs_df(adata, [col_for_color])
         # maybe set color based on type
-        if isinstance(cols[keys[0]].dtype, pd.CategoricalDtype):
+        if isinstance(cols[col_for_color].dtype, pd.CategoricalDtype):
             _maybe_set_colors(
                 source=adata,
                 target=adata,

tests/pl/test_render_points.py

@@ -5,6 +5,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
+import pytest
 import scanpy as sc
 from anndata import AnnData
 from spatialdata import SpatialData, deepcopy
@@ -106,6 +107,14 @@ def test_plot_points_categorical_color(self, sdata_blobs: SpatialData):
         sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")
         sdata_blobs.pl.render_points("blobs_points", color="category").pl.show()
 
+    @pytest.mark.parametrize("method", ["matplotlib", "datashader"])
+    def test_plot_points_categorical_color_column(self, sdata_blobs: SpatialData, method: str):
+        sdata_blobs.pl.render_points("blobs_points", color="genes", method=method).pl.show()
+
+    @pytest.mark.parametrize("method", ["matplotlib", "datashader"])
+    def test_plot_points_continuous_color_column(self, sdata_blobs: SpatialData, method: str):
+        sdata_blobs.pl.render_points("blobs_points", color="instance_id", method=method).pl.show()
+
     def test_plot_datashader_continuous_color(self, sdata_blobs: SpatialData):
         sdata_blobs.pl.render_points(
             element="blobs_points", size=40, color="instance_id", alpha=0.6, method="datashader"