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Published
20 hours ago •
satijalab
satijalab
Issue with the subset function of Seurat handling layers with one cell
Hi,
This is a follow up on issue #8362.
When you subset a Seurat object with multiple layers and end up with one of the samples represented by only one cell, you can no longer subset the object any further. The reason is that the corresponding layers will be vectors rather than matrices (dense or sparse). And the code returns the following error:
Error in methods::slot(object = object, name = "layers")[[layer]][features, :
incorrect number of dimensions
Below is a reproducible code:
require(Seurat)
obj <- pbmc_small
[email protected]$random <- c("a", "a",
sample(x = c("b", "c"),
nrow(x = [email protected]) - 2,
replace = TRUE))
obj[["RNA"]] <- split(x = obj[["RNA"]],
f = [email protected]$random)
obj.g2 <- subset(x = obj,
subset = groups == "g2")
obj.g2.sub <- subset(x = obj.g2,
subset = random %in% c("a", "b"))
And below is my sessionInfo():
> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.1 (2023-06-16)
os macOS Monterey 12.7
system x86_64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Zurich
date 2024-07-01
rstudio 2023.09.0+463 Desert Sunflower (desktop)
pandoc NA
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
caTools 1.18.2 2021-03-28 [1] CRAN (R 4.3.0)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.0)
cluster 2.1.6 2023-12-01 [1] CRAN (R 4.3.0)
clustree 0.5.1 2023-11-05 [1] CRAN (R 4.3.0)
codetools 0.2-20 2024-03-31 [1] CRAN (R 4.3.2)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
cowplot 1.1.3 2024-01-22 [1] CRAN (R 4.3.2)
data.table 1.15.4 2024-03-30 [1] CRAN (R 4.3.2)
deldir 2.0-4 2024-02-28 [1] CRAN (R 4.3.2)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.3.0)
digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.2)
dotCall64 1.1-1 2023-11-28 [1] CRAN (R 4.3.0)
dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.0)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
fastDummies 1.7.3 2023-07-06 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
fitdistrplus 1.1-11 2023-04-25 [1] CRAN (R 4.3.0)
fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0)
future 1.33.2 2024-03-26 [1] CRAN (R 4.3.2)
future.apply 1.11.2 2024-03-28 [1] CRAN (R 4.3.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
ggforce 0.4.2 2024-02-19 [1] CRAN (R 4.3.2)
ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.3.2)
ggraph 2.2.1 2024-03-07 [1] CRAN (R 4.3.2)
ggrepel 0.9.5 2024-01-10 [1] CRAN (R 4.3.0)
ggridges 0.5.6 2024-01-23 [1] CRAN (R 4.3.2)
globals 0.16.3 2024-03-08 [1] CRAN (R 4.3.2)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.0)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.3.0)
gplots 3.1.3.1 2024-02-02 [1] CRAN (R 4.3.2)
graphlayouts 1.1.1 2024-03-09 [1] CRAN (R 4.3.2)
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)
gtools 3.9.5 2023-11-20 [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 4.3.0)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.2)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.3.0)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.3.0)
igraph 2.0.3 2024-03-13 [1] CRAN (R 4.3.2)
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.3.0)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.0)
KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.3.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.0)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.3.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.3.0)
leiden 0.4.3.1 2023-11-17 [1] CRAN (R 4.3.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.0)
listenv 0.9.1 2024-01-29 [1] CRAN (R 4.3.2)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
MASS 7.3-60.0.1 2024-01-13 [1] CRAN (R 4.3.0)
Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.0)
matrixStats 1.2.0 2023-12-11 [1] CRAN (R 4.3.0)
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)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.3.2)
nlme 3.1-164 2023-11-27 [1] CRAN (R 4.3.0)
parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.3.2)
patchwork 1.2.0 2024-01-08 [1] CRAN (R 4.3.0)
pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.0)
plotly 4.10.4 2024-01-13 [1] CRAN (R 4.3.0)
plyr 1.8.9 2023-10-02 [1] CRAN (R 4.3.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
polyclip 1.10-6 2023-09-27 [1] CRAN (R 4.3.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.0)
progressr 0.14.0 2023-08-10 [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)
RANN 2.6.1 2019-01-08 [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 4.3.0)
RcppAnnoy 0.0.22 2024-01-23 [1] CRAN (R 4.3.2)
RcppHNSW 0.6.0 2024-02-04 [1] CRAN (R 4.3.2)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.3.0)
reticulate 1.35.0 2024-01-31 [1] CRAN (R 4.3.2)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.0)
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.3.0)
RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.3.0)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.2)
Rtsne 0.17 2023-12-07 [1] CRAN (R 4.3.0)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.0)
scattermore 1.2 2023-06-12 [1] CRAN (R 4.3.0)
sctransform 0.4.1 2023-10-19 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
Seurat * 5.1.0 2024-05-10 [1] CRAN (R 4.3.3)
SeuratObject * 5.0.2 2024-05-08 [1] CRAN (R 4.3.2)
shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.1)
sp * 2.1-3 2024-01-30 [1] CRAN (R 4.3.2)
spam 2.10-0 2023-10-23 [1] CRAN (R 4.3.0)
spatstat.data 3.0-4 2024-01-15 [1] CRAN (R 4.3.0)
spatstat.explore 3.2-7 2024-03-21 [1] CRAN (R 4.3.2)
spatstat.geom 3.2-9 2024-02-28 [1] CRAN (R 4.3.2)
spatstat.random 3.2-3 2024-02-29 [1] CRAN (R 4.3.2)
spatstat.sparse 3.0-3 2023-10-24 [1] CRAN (R 4.3.0)
spatstat.utils 3.0-4 2023-10-24 [1] CRAN (R 4.3.0)
stringi 1.8.3 2023-12-11 [1] CRAN (R 4.3.0)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.0)
survival 3.5-8 2024-02-14 [1] CRAN (R 4.3.2)
tensor 1.5 2012-05-05 [1] CRAN (R 4.3.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidygraph 1.3.1 2024-01-30 [1] CRAN (R 4.3.2)
tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.2)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.3.2)
tweenr 2.0.3 2024-02-26 [1] CRAN (R 4.3.2)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.0)
usethis 2.2.3 2024-02-19 [1] CRAN (R 4.3.2)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.0)
uwot 0.1.16 2023-06-29 [1] CRAN (R 4.3.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.0)
viridis 0.6.5 2024-01-29 [1] CRAN (R 4.3.2)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
zoo 1.8-12 2023-04-13 [1] CRAN (R 4.3.0)
[1] /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library
Best, Leon
