spatialLIBD
spatialLIBD copied to clipboard
Published
20 hours ago •
LieberInstitute
LieberInstitute
[BUG] `sort_clusters` creates arbitary numeric seqences as legend labels in `vis_grid_clus` plots.
Thanks for the nice package!
I've been using vis_grid_clus to plot multiple samples together. I noticed the legends representing levels of clustervar are always turning to numbers instead of showing their original labels even when I manually set up with colors. With some debugging, I realize the function sort_clusters might be the culprit for it.
library(spatialLIBD)
spe <- fetch_data("spatialDLPFC_Visium_example_subset")
spe$spd <- sprintf("SpD_%02d", spe$BayesSpace_harmony_10)
table(spe$spd)
# SpD_01 SpD_02 SpD_03 SpD_04 SpD_05 SpD_06 SpD_07 SpD_08 SpD_09 SpD_10
# 139 755 1932 2137 1882 688 1805 1511 591 667
sort_clusters(spe$spd) |> table()
# 1 2 3 4 5 6 7 8 9 10
# 2137 1932 1882 1805 1511 755 688 667 591 139
As an end results for vis_grid_clus plots, I'm getting plots with no color filled spots and warning messages 1: No shared levels found between names(values) of the manual scale and the data's fill values. when running the following line.
k <- unique(spe$spd) |> length()
vis_grid_clus(
spe,
"spd",
return_plots = TRUE,
colors = set_names(
Polychrome::palette36.colors(k),
unique(spe$spd) |> sort()
)
)
This is because sort_clusters is employed with the default option of sort_clust = TRUE.
https://github.com/LieberInstitute/spatialLIBD/blob/77a5303f91edb7b9ffb1ce00b4193dae5d16a8a1/R/vis_grid_clus.R#L69-L72
The problem is metigated by making sort_clust = FALSE as well as providing colors option.
vis_grid_clus(
spe,
"spd",
return_plots = TRUE,
sort_clust = FALSE,
colors = set_names(
Polychrome::palette36.colors(k),
unique(spe$spd) |> sort()
)
)
R Session Information
─ Session info ────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 (2023-10-31)
os macOS Sonoma 14.2.1
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-04-23
pandoc 3.1.12.1 @ /opt/homebrew/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
AnnotationDbi 1.64.1 2023-11-02 [1] Bioconductor
AnnotationHub 3.10.0 2023-10-26 [1] Bioconductor
attempt 0.3.1 2020-05-03 [1] CRAN (R 4.3.0)
beachmat 2.18.1 2024-02-17 [1] Bioconductor 3.18 (R 4.3.2)
beeswarm 0.4.0 2021-06-01 [1] CRAN (R 4.3.0)
benchmarkme 1.0.8 2022-06-12 [1] CRAN (R 4.3.0)
benchmarkmeData 1.0.4 2020-04-23 [1] CRAN (R 4.3.0)
Biobase * 2.62.0 2023-10-26 [1] Bioconductor
BiocFileCache 2.10.1 2023-10-26 [1] Bioconductor
BiocGenerics * 0.48.1 2023-11-02 [1] Bioconductor
BiocIO 1.12.0 2023-10-26 [1] Bioconductor
BiocManager 1.30.22 2023-08-08 [1] CRAN (R 4.3.0)
BiocNeighbors 1.20.2 2024-01-13 [1] Bioconductor 3.18 (R 4.3.2)
BiocParallel 1.36.0 2023-10-26 [1] Bioconductor
BiocSingular 1.18.0 2023-10-24 [1] Bioconductor
BiocVersion 3.18.1 2023-11-18 [1] Bioconductor 3.18 (R 4.3.2)
Biostrings 2.70.1 2023-10-26 [1] Bioconductor
bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.3.0)
bslib 0.7.0 2024-03-29 [1] CRAN (R 4.3.1)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1)
codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.2)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
config 0.3.2 2023-08-30 [1] CRAN (R 4.3.0)
cowplot 1.1.2 2023-12-15 [1] CRAN (R 4.3.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
curl 5.2.0 2023-12-08 [1] CRAN (R 4.3.1)
data.table 1.14.10 2023-12-08 [1] CRAN (R 4.3.1)
DBI 1.2.0 2023-12-21 [1] CRAN (R 4.3.1)
dbplyr 2.4.0 2023-10-26 [1] CRAN (R 4.3.1)
DelayedArray 0.28.0 2023-10-24 [1] Bioconductor
DelayedMatrixStats 1.24.0 2023-10-24 [1] Bioconductor
digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.3.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.3.1)
DT 0.31 2023-12-09 [1] CRAN (R 4.3.1)
edgeR 4.0.16 2024-02-20 [1] Bioconductor 3.18 (R 4.3.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
ExperimentHub 2.10.0 2023-10-26 [1] Bioconductor
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.1)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fields 15.2 2023-08-17 [1] CRAN (R 4.3.0)
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.3.1)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.3.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.38.8 2024-03-16 [1] Bioconductor 3.18 (R 4.3.3)
GenomeInfoDbData 1.2.11 2023-11-08 [1] Bioconductor
GenomicAlignments 1.38.0 2023-10-26 [1] Bioconductor
GenomicRanges * 1.54.1 2023-10-30 [1] Bioconductor
ggbeeswarm 0.7.2 2023-04-29 [1] CRAN (R 4.3.0)
ggplot2 * 3.5.0 2024-02-23 [1] CRAN (R 4.3.1)
ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.3.1)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1)
golem 0.4.1 2023-06-05 [1] CRAN (R 4.3.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.0)
gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.1)
httpuv 1.6.13 2023-12-06 [1] CRAN (R 4.3.1)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
interactiveDisplayBase 1.40.0 2023-10-26 [1] Bioconductor
IRanges * 2.36.0 2023-10-26 [1] Bioconductor
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.2)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1)
KEGGREST 1.42.0 2023-10-26 [1] Bioconductor
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.1)
lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.0)
limma 3.58.1 2023-11-02 [1] Bioconductor
locfit 1.5-9.9 2024-03-01 [1] CRAN (R 4.3.1)
lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.3.1)
magick 2.8.2 2023-12-20 [1] CRAN (R 4.3.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
maps 3.4.2 2023-12-15 [1] CRAN (R 4.3.1)
Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.2)
MatrixGenerics * 1.14.0 2023-10-26 [1] Bioconductor
matrixStats * 1.2.0 2023-12-11 [1] CRAN (R 4.3.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.1)
paletteer 1.5.0 2022-10-19 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
plotly 4.10.3 2023-10-21 [1] CRAN (R 4.3.1)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
Polychrome * 1.5.1 2022-05-03 [1] CRAN (R 4.3.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.3.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1)
RCurl 1.98-1.14 2024-01-09 [1] CRAN (R 4.3.1)
readr * 2.1.4 2023-02-10 [1] CRAN (R 4.3.0)
rematch2 2.1.2 2020-05-01 [1] CRAN (R 4.3.0)
restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1)
Rsamtools 2.18.0 2023-10-26 [1] Bioconductor
RSQLite 2.3.4 2023-12-08 [1] CRAN (R 4.3.1)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.1)
rsvd 1.0.5 2021-04-16 [1] CRAN (R 4.3.0)
rtracklayer 1.62.0 2023-10-26 [1] Bioconductor
S4Arrays 1.2.1 2024-03-05 [1] Bioconductor 3.18 (R 4.3.2)
S4Vectors * 0.40.2 2023-11-25 [1] Bioconductor 3.18 (R 4.3.2)
sass 0.4.9 2024-03-15 [1] CRAN (R 4.3.1)
ScaledMatrix 1.10.0 2023-10-24 [1] Bioconductor
scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1)
scater 1.30.1 2023-11-16 [1] Bioconductor
scatterplot3d 0.3-44 2023-05-05 [1] CRAN (R 4.3.0)
scuttle 1.12.0 2023-10-24 [1] Bioconductor
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shiny 1.8.0 2023-11-17 [1] CRAN (R 4.3.1)
shinyWidgets 0.8.0 2023-08-30 [1] CRAN (R 4.3.0)
SingleCellExperiment * 1.24.0 2023-10-24 [1] Bioconductor
spam 2.10-0 2023-10-23 [1] CRAN (R 4.3.1)
SparseArray 1.2.4 2024-02-10 [1] Bioconductor 3.18 (R 4.3.2)
sparseMatrixStats 1.14.0 2023-10-26 [1] Bioconductor
SpatialExperiment * 1.12.0 2023-10-26 [1] Bioconductor
spatialLIBD * 1.14.1 2023-11-30 [1] Bioconductor 3.18 (R 4.3.0)
statmod 1.5.0 2023-01-06 [1] CRAN (R 4.3.0)
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.1)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.3.1)
SummarizedExperiment * 1.32.0 2023-10-24 [1] Bioconductor
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.3.0)
timechange 0.2.0 2023-01-11 [1] CRAN (R 4.3.0)
tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.3.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1)
vipor 0.4.7 2023-12-18 [1] CRAN (R 4.3.1)
viridis 0.6.5 2024-01-29 [1] CRAN (R 4.3.1)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1)
XML 3.99-0.16 2023-11-29 [1] CRAN (R 4.3.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector 0.42.0 2023-10-26 [1] Bioconductor
yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1)
zlibbioc 1.48.2 2024-03-19 [1] Bioconductor 3.18 (R 4.3.3)
[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
───────────────────────────────────────────────────────────────────────────────────────────────
