plotLegend not showing #142
Description
Describe the bug
It seems that legend cannot be plotted with plotLegend function. There's no error message, but the legend does not show on plot.
Reproducible example
It is not working even with example data.
R session info
─ Session info ───────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.2 (2024-10-31)
os CentOS Linux 7 (Core)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2025-08-29
rstudio 2023.12.1+402 Ocean Storm (server)
pandoc 3.5 @ /scratch/z/zm104/miniforge3/envs/seurat5/bin/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [1] CRAN (R 4.4.1)
AnnotationDbi * 1.66.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
AnnotationFilter 1.26.0 2023-10-24 [1] Bioconductor
backports 1.5.0 2024-05-23 [1] CRAN (R 4.4.1)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.4.1)
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.4.1)
Biobase * 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
BiocFileCache 2.10.2 2024-03-27 [1] Bioconductor 3.18 (R 4.4.1)
BiocGenerics * 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
BiocIO 1.14.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
BiocParallel 1.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
biomaRt 2.60.1 2024-06-26 [1] Bioconductor 3.19 (R 4.4.1)
Biostrings 2.72.1 2024-06-02 [1] Bioconductor 3.19 (R 4.4.1)
biovizBase 1.50.0 2023-10-24 [1] Bioconductor
bit 4.5.0 2024-09-20 [1] CRAN (R 4.4.1)
bit64 4.5.2 2024-09-22 [1] CRAN (R 4.4.1)
bitops 1.0-8 2024-07-29 [1] CRAN (R 4.4.1)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.1)
BSgenome 1.70.2 2024-02-08 [1] Bioconductor 3.18 (R 4.4.1)
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.1)
checkmate 2.3.2 2024-07-29 [1] CRAN (R 4.4.1)
cli 3.6.4 2025-02-13 [1] CRAN (R 4.4.1)
cluster 2.1.6 2023-12-01 [1] CRAN (R 4.4.1)
codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.1)
colorspace * 2.1-1 2024-07-26 [1] CRAN (R 4.4.1)
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.1)
curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.1)
data.table * 1.15.4 2024-03-30 [1] CRAN (R 4.4.1)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.1)
dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.1)
DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.1)
deldir 2.0-4 2024-02-28 [1] CRAN (R 4.4.1)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.1)
dichromat 2.0-0.1 2022-05-02 [1] CRAN (R 4.4.1)
digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.4.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.1)
dynamicTreeCut 1.63-1 2016-03-11 [1] CRAN (R 4.4.1)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.1)
ensembldb 2.26.0 2023-10-24 [1] Bioconductor
evaluate 1.0.3 2025-01-10 [1] CRAN (R 4.4.1)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.1)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.1)
fastcluster 1.3.0 2025-05-07 [1] CRAN (R 4.4.1)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.1)
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.1)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.1)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.4.1)
foreign 0.8-87 2024-06-26 [1] CRAN (R 4.4.1)
Formula 1.2-5 2023-02-24 [1] CRAN (R 4.4.1)
fs 1.6.5 2024-10-30 [1] CRAN (R 4.4.1)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.1)
GenomeInfoDb * 1.40.1 2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
GenomeInfoDbData 1.2.12 2024-08-15 [1] Bioconductor
GenomicAlignments 1.40.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
GenomicFeatures * 1.56.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
GenomicInteractions * 1.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
GenomicRanges * 1.56.1 2024-06-12 [1] Bioconductor 3.19 (R 4.4.1)
ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.4.1)
ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.4.1)
ggplotify 0.1.2 2023-08-09 [1] CRAN (R 4.4.1)
ggrastr 1.0.2 2023-06-01 [1] CRAN (R 4.4.1)
glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.1)
GO.db 3.19.1 2024-11-18 [1] Bioconductor
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.1)
gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.4.1)
gtable 0.3.6 2024-10-25 [1] CRAN (R 4.4.1)
Gviz * 1.51.0 2025-06-03 [1] Github (ivanek/Gviz@26ea19f)
Hmisc 5.2-3 2025-03-16 [1] CRAN (R 4.4.1)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.1)
htmlTable 2.4.3 2024-07-21 [1] CRAN (R 4.4.1)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.1)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.1)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.1)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.1)
httr2 1.0.5 2024-09-26 [1] CRAN (R 4.4.1)
igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.1)
impute 1.78.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
InteractionSet * 1.32.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
interp 1.1-6 2024-01-26 [1] CRAN (R 4.4.1)
IRanges * 2.38.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.4.1)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.4.1)
jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.4.1)
jsonlite 1.9.1 2025-03-03 [1] CRAN (R 4.4.1)
KEGGREST 1.44.1 2024-06-19 [1] Bioconductor 3.19 (R 4.4.1)
knitr 1.50 2025-03-16 [1] CRAN (R 4.4.1)
labeling 0.4.3 2023-08-29 [1] CRAN (R 4.4.1)
later 1.3.2 2023-12-06 [1] CRAN (R 4.4.1)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.1)
latticeExtra 0.6-30 2022-07-04 [1] CRAN (R 4.4.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.4.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.1)
lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.4.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.1)
Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.4.1)
MatrixGenerics * 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
matrixStats * 1.5.0 2025-01-07 [1] CRAN (R 4.4.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.1)
mime 0.13 2025-03-17 [1] CRAN (R 4.4.1)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.1)
mixsqp 0.3-54 2023-12-20 [1] CRAN (R 4.4.1)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.1)
nnet 7.3-19 2023-05-03 [1] CRAN (R 4.4.1)
org.Hs.eg.db 3.19.1 2025-01-03 [1] Bioconductor
patchwork * 1.3.0 2024-09-16 [1] CRAN (R 4.4.1)
Phoenix * 0.1.0 2024-10-25 [1] local
pillar 1.10.1 2025-01-07 [1] CRAN (R 4.4.1)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.1)
pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.4.1)
plotgardener * 1.10.2 2024-06-30 [1] Bioconductor 3.19 (R 4.4.1)
plotgardenerData * 1.10.0 2024-05-02 [1] Bioconductor 3.19 (R 4.4.1)
plyr 1.8.9 2023-10-02 [1] CRAN (R 4.4.1)
plyranges * 1.24.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
png 0.1-8 2022-11-29 [1] CRAN (R 4.4.1)
preprocessCore 1.66.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
PrettyCols * 1.1.0.9001 2024-08-18 [1] Github (nrennie/PrettyCols@47e9516)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.4.1)
profvis 0.4.0 2024-09-20 [1] CRAN (R 4.4.1)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.1)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.1)
ProtGenerics 1.34.0 2023-10-24 [1] Bioconductor
purrr * 1.0.4 2025-02-05 [1] CRAN (R 4.4.1)
R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.1)
R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.1)
R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.1)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.4.1)
ragg 1.3.3 2024-09-11 [1] CRAN (R 4.4.1)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.4.1)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.1)
Rcpp 1.0.14 2025-01-12 [1] CRAN (R 4.4.1)
RcppParallel 5.1.9 2024-08-19 [1] CRAN (R 4.4.1)
RCurl 1.98-1.16 2024-07-11 [1] CRAN (R 4.4.1)
readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.1)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.1)
reshape 0.8.9 2022-04-12 [1] CRAN (R 4.4.1)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.4.1)
Rfast 2.1.5.1 2025-03-14 [1] CRAN (R 4.4.1)
rjson 0.2.22 2024-08-20 [1] CRAN (R 4.4.1)
rlang 1.1.5 2025-01-17 [1] CRAN (R 4.4.1)
rmarkdown 2.29 2024-11-04 [1] CRAN (R 4.4.1)
rpart 4.1.23 2023-12-05 [1] CRAN (R 4.4.1)
Rsamtools 2.20.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.4.1)
rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.4.1)
rtracklayer 1.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
S4Arrays 1.4.1 2024-05-20 [1] Bioconductor 3.19 (R 4.4.1)
S4Vectors * 0.42.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.1)
shiny 1.9.1 2024-08-01 [1] CRAN (R 4.4.1)
SparseArray 1.4.8 2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
strawr 0.0.92 2024-07-16 [1] CRAN (R 4.4.1)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.1)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.1)
SummarizedExperiment * 1.34.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
survival 3.7-0 2024-06-05 [1] CRAN (R 4.4.1)
susieR * 0.12.46 2025-06-01 [1] Github (stephenslab/susieR@6664eb2)
systemfonts 1.2.1 2025-01-20 [1] CRAN (R 4.4.1)
textshaping 1.0.0 2025-01-20 [1] CRAN (R 4.4.1)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.4.1)
tidyCoverage * 1.0.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
tidyplots * 0.3.1.9000 2025-07-08 [1] Github (jbengler/tidyplots@5c6614d)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.1)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.1)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.1)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.1)
TxDb.Hsapiens.UCSC.hg38.knownGene * 3.18.0 2025-07-15 [1] Bioconductor
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.4.1)
UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.1)
usethis 3.0.0 2024-07-29 [1] CRAN (R 4.4.1)
VariantAnnotation 1.48.1 2023-11-15 [1] Bioconductor
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.1)
vipor 0.4.7 2023-12-18 [1] CRAN (R 4.4.1)
WGCNA 1.73 2024-09-18 [1] CRAN (R 4.4.1)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
xfun 0.51 2025-02-19 [1] CRAN (R 4.4.1)
XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.4.1)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.1)
XVector 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
yaml 2.3.10 2024-07-26 [1] CRAN (R 4.4.1)
yulab.utils 0.1.8 2024-11-07 [1] CRAN (R 4.4.1)
zigg 0.0.2 2025-02-07 [1] CRAN (R 4.4.1)
zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
[1] /scratch/z/zm104/miniforge3/envs/seurat5/lib/R/library
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