the " SpatialDimPlot()" is picture have a problem?---Spatial Data

[jinyuanchun]

i follow the "Estimating Microenvironment from Spatial Data" doc. , but SpatialDimPlot() have a problem

[jcyang34]

I am not able to reproduce this. Can you provide your sessionInfo()? It could be a similar issue mentioned in satijalab/seurat#4102, I wonder if the workarounds there work for you.

[jinyuanchun]

info is

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /storeData/BioLab/software/miniconda3/envs/R-4.1.0/lib/libopenblasp-r0.3.21.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] viridis_0.6.2 viridisLite_0.4.1
[3] NICHES_1.0.0 SeuratWrappers_0.3.0
[5] dplyr_1.0.10 patchwork_1.1.2
[7] cowplot_1.1.1 ggplot2_3.3.6
[9] stxBrain.SeuratData_0.1.1 SeuratData_0.2.2
[11] sp_1.5-0 SeuratObject_4.1.1
[13] Seurat_4.1.1

loaded via a namespace (and not attached):
[1] uuid_1.1-0 backports_1.4.1 plyr_1.8.7
[4] igraph_1.3.4 repr_1.1.4 lazyeval_0.2.2
[7] splines_4.1.3 listenv_0.8.0 scattermore_0.8
[10] digest_0.6.29 htmltools_0.5.3 fansi_1.0.3
[13] magrittr_2.0.3 tensor_1.5 cluster_2.1.3
[16] ROCR_1.0-11 remotes_2.4.2 globals_0.16.1
[19] matrixStats_0.62.0 R.utils_2.12.0 spatstat.sparse_2.1-1
[22] colorspace_2.0-3 rappdirs_0.3.3 ggrepel_0.9.1
[25] crayon_1.5.1 jsonlite_1.8.0 progressr_0.11.0
[28] spatstat.data_2.2-0 survival_3.4-0 zoo_1.8-10
[31] glue_1.6.2 polyclip_1.10-0 gtable_0.3.1
[34] leiden_0.4.2 car_3.1-0 future.apply_1.9.0
[37] abind_1.4-5 scales_1.2.1 rstatix_0.7.0
[40] spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.9
[43] xtable_1.8-4 reticulate_1.26 spatstat.core_2.4-4
[46] rsvd_1.0.5 htmlwidgets_1.5.4 httr_1.4.4
[49] RColorBrewer_1.1-3 ellipsis_0.3.2 ica_1.0-3
[52] pkgconfig_2.0.3 R.methodsS3_1.8.2 farver_2.1.1
[55] uwot_0.1.14 deldir_1.0-6 utf8_1.2.2
[58] tidyselect_1.1.2 labeling_0.4.2 rlang_1.0.5
[61] reshape2_1.4.4 later_1.3.0 munsell_0.5.0
[64] tools_4.1.3 cli_3.3.0 generics_0.1.3
[67] broom_1.0.1 ggridges_0.5.3 evaluate_0.16
[70] stringr_1.4.1 fastmap_1.1.0 goftest_1.2-3
[73] fitdistrplus_1.1-8 purrr_0.3.4 RANN_2.6.1
[76] pbapply_1.5-0 future_1.28.0 nlme_3.1-159
[79] mime_0.12 R.oo_1.25.0 compiler_4.1.3
[82] plotly_4.10.0 png_0.1-7 ggsignif_0.6.3
[85] spatstat.utils_2.3-1 tibble_3.1.8 stringi_1.7.8
[88] rgeos_0.5-9 lattice_0.20-45 IRdisplay_1.1
[91] Matrix_1.4-1 vctrs_0.4.1 pillar_1.8.1
[94] lifecycle_1.0.1 BiocManager_1.30.18 spatstat.geom_2.4-0
[97] lmtest_0.9-40 RcppAnnoy_0.0.19 data.table_1.14.2
[100] irlba_2.3.5 httpuv_1.6.5 R6_2.5.1
[103] promises_1.2.0.1 KernSmooth_2.23-20 gridExtra_2.3
[106] parallelly_1.32.1 codetools_0.2-18 MASS_7.3-58.1
[109] withr_2.5.0 sctransform_0.3.4 mgcv_1.8-40
[112] parallel_4.1.3 grid_4.1.3 rpart_4.1.16
[115] IRkernel_1.3 tidyr_1.2.0 carData_3.0-5
[118] Rtsne_0.16 ggpubr_0.4.0 pbdZMQ_0.3-7
[121] shiny_1.7.2 base64enc_0.1-3

[jcyang34]

Ok, I am able to reproduce the bug. It appears to be a bug of SpatialDimPlot() in Seurat v4.1.1 and onwards when group.by is set to metadata other than idents, as mentioned in satijalab/seurat#6179.

Since here the idents is also seurat_clusters, a workaround is to just remove the group.by = seurat_clusters in SpatialDimPlot() and it should solve the problem. I think the Seurat team will soon fix this bug.

[jinyuanchun]

thanks, it ok