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satijalab
A bunch of bugs in Spatial-Plots!
Hi, I found many BUGs in Spatial-related plotting functions in Seurat v4.0+ which are not in v3.6.
1. 'crop=True' produces irregular size of image figure! This issue was already reported many times: https://github.com/satijalab/seurat/issues/5141 https://github.com/satijalab/seurat/issues/5543
2. In SpatialDimPlot, 'group.by' parameter doesn't work, and must set 'Idents' before!
seu <- LoadData("stxBrain", type = "anterior1")
[email protected]$g1 <- sample(c("A","B"), ncol(seu), replace=T)
SpatialDimPlot(seu, group.by="g1", pt.size.factor=1, label=T, label.size=8)
Idents(seu) <- "g1"
SpatialDimPlot(seu, pt.size.factor=1, label=T, label.size=8)
3. In SpatialDimPlot, setting 'cols' would raise an error!
SpatialDimPlot(seu, pt.size.factor=1, label=T, label.size=8, cols=c("#E64B35FF","#4DBBD5FF"))
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /share/modules/R/R-4.1.2/lib/R/lib/libRblas.so
LAPACK: /share/modules/R/R-4.1.2/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] stxBrain.SeuratData_0.1.1 pbmc3k.SeuratData_3.1.4 SeuratData_0.2.1 SingleCellExperiment_1.16.0 SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1
[8] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.62.0 sp_1.4-7
[15] SeuratObject_4.1.0 Seurat_4.1.1 ggfittext_0.9.1 ggrastr_1.0.1 ggsci_2.9 ggpubr_0.4.0 tictoc_1.0.1
[22] doParallel_1.0.17 iterators_1.0.14 foreach_1.5.2 R.utils_2.11.0 R.oo_1.24.0 R.methodsS3_1.8.1 forcats_0.5.1
[29] readr_2.1.2 tidyr_1.2.0 tibble_3.1.7 ggplot2_3.3.6 tidyverse_1.3.1 furrr_0.3.0 future_1.25.0
[36] purrr_0.3.4 stringr_1.4.0 dplyr_1.0.9 plyr_1.8.7 reshape2_1.4.4 colorout_1.2-2
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.25 tidyselect_1.1.2 htmlwidgets_1.5.4 grid_4.1.2 Rtsne_0.16 munsell_0.5.0 codetools_0.2-18 ica_1.0-2
[10] miniUI_0.1.1.1 withr_2.5.0 spatstat.random_2.2-0 colorspace_2.0-3 progressr_0.10.0 knitr_1.39 rstudioapi_0.13 ROCR_1.0-11 ggsignif_0.6.3
[19] tensor_1.5 listenv_0.8.0 labeling_0.4.2 GenomeInfoDbData_1.2.7 polyclip_1.10-0 farver_2.1.0 parallelly_1.31.1 vctrs_0.4.1 generics_0.1.2
[28] xfun_0.31 R6_2.5.1 ggbeeswarm_0.6.0 bitops_1.0-7 spatstat.utils_2.3-1 DelayedArray_0.20.0 assertthat_0.2.1 promises_1.2.0.1 scales_1.2.0
[37] rgeos_0.5-9 beeswarm_0.4.0 gtable_0.3.0 globals_0.15.0 goftest_1.2-3 rlang_1.0.2 splines_4.1.2 rstatix_0.7.0 lazyeval_0.2.2
[46] spatstat.geom_2.4-0 broom_0.8.0 yaml_2.3.5 abind_1.4-5 modelr_0.1.8 backports_1.4.1 httpuv_1.6.5 tools_4.1.2 ellipsis_0.3.2
[55] spatstat.core_2.4-2 RColorBrewer_1.1-3 ggridges_0.5.3 Rcpp_1.0.8.3 zlibbioc_1.40.0 RCurl_1.98-1.6 rpart_4.1.16 deldir_1.0-6 pbapply_1.5-0
[64] cowplot_1.1.1 zoo_1.8-10 haven_2.5.0 ggrepel_0.9.1 cluster_2.1.3 fs_1.5.2 magrittr_2.0.3 RSpectra_0.16-1 data.table_1.14.2
[73] scattermore_0.8 lmtest_0.9-40 reprex_2.0.1 RANN_2.6.1 fitdistrplus_1.1-8 hms_1.1.1 patchwork_1.1.1 mime_0.12 evaluate_0.15
[82] xtable_1.8-4 RhpcBLASctl_0.21-247.1 readxl_1.4.0 gridExtra_2.3 compiler_4.1.2 KernSmooth_2.23-20 crayon_1.5.1 htmltools_0.5.2 mgcv_1.8-40
[91] later_1.3.0 tzdb_0.3.0 lubridate_1.8.0 DBI_1.1.2 dbplyr_2.1.1 rappdirs_0.3.3 MASS_7.3-57 Matrix_1.4-1 car_3.0-13
[100] cli_3.3.0 igraph_1.3.1 pkgconfig_2.0.3 plotly_4.10.0 spatstat.sparse_2.1-1 xml2_1.3.3 vipor_0.4.5 XVector_0.34.0 rvest_1.0.2
[109] digest_0.6.29 sctransform_0.3.3 RcppAnnoy_0.0.19 spatstat.data_2.2-0 rmarkdown_2.14 cellranger_1.1.0 leiden_0.4.2 uwot_0.1.11 shiny_1.7.1
[118] lifecycle_1.0.1 nlme_3.1-157 jsonlite_1.8.0 carData_3.0-5 viridisLite_0.4.0 fansi_1.0.3 pillar_1.7.0 lattice_0.20-45 fastmap_1.1.0
[127] httr_1.4.3 survival_3.3-1 glue_1.6.2 png_0.1-7 stringi_1.7.6 irlba_2.3.5 future.apply_1.9.0
Hi Seurat team. I just want to echo point 3 by QqQss, the issue with colors and SpatialDimPlot. I also saw this in Seurat v4.1.0 (but not with plain DimPlot). When I downgraded to Seurat v4.0.6, the problem resolved. Thanks for working on this! Best- Orr
Hi Seurat team, thank you so much for your amazing work!!! I'm also seeing the above bugs in Seurat 4.1.1. Thank you for looking into this!
Hi Seurat, pinging this issue again cause I'm having the exact same issue in Seurat 4.1.1! I would be great to have a fix!
