Issue Description
Hi Seurat Team (tagging @anashen @YoukaiFromAccounting here),
Following the merge of #10028 the label.box parameter in DimPlot (passed to LabelClusters no longer properly colors the filled boxes. Given the changes made spatial plotting there I wanted to leave this one to Seurat team for how you would like to handle fix. Issue comes in that the scale_fill_manual line was removed from LabelClusters if box = TRUE. This is because the color column in the "labels.loc" data.frame no longer contains valid color values.
Hence just restoring that line then spits the following error:
Error in `geom.use()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 2nd layer.
Caused by error:
! Unknown colour name: -5.69291337379421
Again just wanted to leave this one with you all to figure out how to handle with the updates/changes to spatial plotting.
Thanks!
Best,
Sam
Reproducing Code Example
library(Seurat)
DimPlot(pbmc_small, label.box = T, pt.size = 0.25, label.size = 5, label = T, cols = DiscretePalette(n = 3, palette = "polychrome"))
Error Message
Additional Comments
No response
Session Info
> sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cowplot_1.2.0 rliger_2.2.1 beepr_2.0 reticulate_1.43.0 qs2_0.1.5 patchwork_1.3.2 scCustomize_3.2.1.0019 SeuratWrappers_0.4.0
[9] Seurat_5.3.1.9999 SeuratObject_5.1.0 sp_2.2-0 lubridate_1.9.4 forcats_1.0.1 stringr_1.5.2 dplyr_1.1.4 purrr_1.1.0
[17] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 ggplot2_4.0.0 tidyverse_2.0.0 rlang_1.1.6
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.5.0 later_1.4.4 prismatic_1.1.2 R.oo_1.27.1 polyclip_1.10-7 janitor_2.2.1 fastDummies_1.7.5
[9] lifecycle_1.0.4 globals_0.18.0 processx_3.8.6 lattice_0.22-7 MASS_7.3-65 magrittr_2.0.4 plotly_4.11.0 remotes_2.5.0
[17] httpuv_1.6.16 sctransform_0.4.2 spam_2.11-1 sessioninfo_1.2.3 pkgbuild_1.4.8 spatstat.sparse_3.1-0 pbapply_1.7-4 RColorBrewer_1.1-3
[25] abind_1.4-8 pkgload_1.4.1 audio_0.1-11 Rtsne_0.17 R.utils_2.13.0 BiocGenerics_0.54.0 circlize_0.4.16 IRanges_2.42.0
[33] S4Vectors_0.46.0 ggrepel_0.9.6 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.2-0 goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.4-2
[41] fitdistrplus_1.2-4 parallelly_1.45.1 DelayedArray_0.34.1 codetools_0.2-20 RApiSerialize_0.1.4 tidyselect_1.2.1 shape_1.4.6.1 farver_2.1.2
[49] stats4_4.5.0 matrixStats_1.5.0 spatstat.explore_3.5-3 jsonlite_2.0.0 ellipsis_0.3.2 progressr_0.15.1 ggridges_0.5.7 survival_3.8-3
[57] tools_4.5.0 ica_1.0-3 Rcpp_1.1.0 glue_1.8.0 SparseArray_1.8.0 gridExtra_2.3 MatrixGenerics_1.20.0 usethis_3.2.1
[65] HDF5Array_1.36.0 withr_3.0.2 BiocManager_1.30.26 fastmap_1.2.0 rhdf5filters_1.20.0 callr_3.7.6 digest_0.6.37 rsvd_1.0.5
[73] timechange_0.3.0 R6_2.6.1 mime_0.13 ggprism_1.0.7 colorspace_2.1-2 scattermore_1.2 tensor_1.5.1 dichromat_2.0-0.1
[81] spatstat.data_3.1-8 h5mread_1.0.1 R.methodsS3_1.8.2 generics_0.1.4 data.table_1.17.8 S4Arrays_1.8.0 httr_1.4.7 htmlwidgets_1.6.4
[89] uwot_0.2.3 pkgconfig_2.0.3 gtable_0.3.6 lmtest_0.9-40 S7_0.2.0 XVector_0.48.0 htmltools_0.5.8.1 dotCall64_1.2
[97] scales_1.4.0 png_0.1-8 spatstat.univar_3.1-4 snakecase_0.11.1 rstudioapi_0.17.1 tzdb_0.5.0 reshape2_1.4.4 nlme_3.1-168
[105] curl_7.0.0 rhdf5_2.52.0 cachem_1.1.0 zoo_1.8-14 GlobalOptions_0.1.2 KernSmooth_2.23-26 parallel_4.5.0 miniUI_0.1.2
[113] vipor_0.4.7 ggrastr_1.0.2 desc_1.4.3 pillar_1.11.1 grid_4.5.0 vctrs_0.6.5 RANN_2.6.2 promises_1.3.3
[121] stringfish_0.17.0 xtable_1.8-4 cluster_2.1.8.1 beeswarm_0.4.0 paletteer_1.6.0 cli_3.6.5 compiler_4.5.0 crayon_1.5.3
[129] future.apply_1.20.0 labeling_0.4.3 rematch2_2.1.2 ps_1.9.1 plyr_1.8.9 fs_1.6.6 ggbeeswarm_0.7.2 stringi_1.8.7
[137] viridisLite_0.4.2 deldir_2.0-4 lazyeval_0.2.2 devtools_2.4.6 spatstat.geom_3.6-0 Matrix_1.7-4 RcppHNSW_0.6.0 hms_1.1.3
[145] future_1.67.0 Rhdf5lib_1.30.0 shiny_1.11.1 qs_0.27.3 ROCR_1.0-11 igraph_2.1.4 memoise_2.0.1 RcppParallel_5.1.11-1
Issue Description
Hi Seurat Team (tagging @anashen @YoukaiFromAccounting here),
Following the merge of #10028 the
label.boxparameter inDimPlot(passed toLabelClustersno longer properly colors the filled boxes. Given the changes made spatial plotting there I wanted to leave this one to Seurat team for how you would like to handle fix. Issue comes in that thescale_fill_manualline was removed fromLabelClustersifbox = TRUE. This is because the color column in the "labels.loc" data.frame no longer contains valid color values.Hence just restoring that line then spits the following error:
Again just wanted to leave this one with you all to figure out how to handle with the updates/changes to spatial plotting.
Thanks!
Best,
Sam
Reproducing Code Example
Error Message
Additional Comments
No response
Session Info