A bunch of bugs in Spatial-Plots!

[QqQss]

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:
#5141
#5543

2. In SpatialDimPlot, 'group.by' parameter doesn't work, and must set 'Idents' before!

seu <- LoadData("stxBrain", type = "anterior1")
seu@meta.data$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  

[orrzor]

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

[MarcElosua]

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!

[MohamedAbdalfatah]

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!

[dcollins15]

Thanks for using Seurat!

It appears that this issue has gone stale. In an effort to keep our Issues board from getting more unruly than it already is, we’re going to begin closing out issues that haven’t had any activity since the release of v4.4.0.

If this issue is still relevant we strongly encourage you to reopen or repost it, especially if you didn’t initially receive a response from us.