plotCoregulationProfileSpatial for Seurat5 object with layers

[csmoreno]

When I run this code
ps <- plotCoregulationProfileSpatial(pathways[topPathways], CM01.object, title=titles)

or this code
ps <- plotCoregulationProfileSpatial(pathways[topPathways], CM01.object, title=titles, assay = "Spatial.016um")

on a Seurat5 Object that has scaled data in it under
CM01.object@assays$Spatial.016um$scale.data

I get this error:
Error in addGesecaScores(list(pathway = pathway), object, assay = assay, :
no slot of name "scale.data" for this object of class "Assay5"

I think it might have to do with the use of layers in Seurat5. Any idea how to fix this?

Thanks

[vdsukhov]

Hey @csmoreno,

Could you please share the Seurat object you're working with (you can send it to me via email in case you don't want to make it publicly available: [email protected]) and some minimal code snippet example which causes an error so I can try to reproduce the error on my end? It would also be great if you could include the output of sessionInfo() from your R session.

[csmoreno]

Hi Vladimir,
The object is too big to upload, but I can email you a link to download it.

Here is the code:

library(tidyverse)
library(purrr)
library("fgsea")
library(RColorBrewer)
library(Seurat)
library(SeuratObject)
library(SeuratData)
library(ggplot2)
library(patchwork)
library(dplyr)
library(Rfast)
library(Rfast2)
library(sctransform)
library(SeuratWrappers)
library(Banksy)
library(spacexr)
library(msigdbr)

CM01.object = readRDS('./rds_objects/CM01.object.16um.rds')
Assays(CM01.object)
DefaultAssay(CM01.object) <- "Spatial.016um"

fGSEA analysis

Hallmark_pathwaysDF <- msigdbr("human", category="H")
Hallmark_pathways <- split(Hallmark_pathwaysDF$gene_symbol, Hallmark_pathwaysDF$gs_name)

run spatial fgsea

set.seed(1)
E <- CM01.object@reductions$[email protected]
geseca_HALLMARK_Res <- geseca(Hallmark_pathways, E, minSize = 15, maxSize = 500, center = FALSE)
head(geseca_HALLMARK_Res, 10)

###plot top four Hallmark pathways
topPathways <- geseca_HALLMARK_Res[, pathway] |> head(4)
titles <- sub("HALLMARK_", "", topPathways)

ps <- plotCoregulationProfileSpatial(Hallmark_pathways[topPathways], CM01.object, title=titles)

cowplot::plot_grid(plotlist=ps, ncol=2)

sessionInfo()

And here is the sessionInfo:

R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

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] msigdbr_7.5.1 spacexr_2.2.1 Banksy_1.1.0
[4] SeuratWrappers_0.3.5 sctransform_0.4.1 Rfast2_0.1.5.2
[7] Rfast_2.1.0 RcppParallel_5.1.9 RcppZiggurat_0.1.6
[10] Rcpp_1.0.13-1 patchwork_1.3.0 stxBrain.SeuratData_0.1.2
[13] SeuratData_0.2.2.9001 Seurat_5.1.0 SeuratObject_5.0.2
[16] sp_2.1-4 RColorBrewer_1.1-3 fgsea_1.30.0
[19] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[22] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[25] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1
[28] tidyverse_2.0.0

loaded via a namespace (and not attached):
[1] RcppHungarian_0.3 RcppAnnoy_0.0.22 splines_4.4.1
[4] later_1.3.2 R.oo_1.27.0 polyclip_1.10-7
[7] fastDummies_1.7.4 lifecycle_1.0.4 aricode_1.0.3
[10] doParallel_1.0.17 globals_0.16.3 Rnanoflann_0.0.3
[13] lattice_0.22-6 MASS_7.3-61 magrittr_2.0.3
[16] plotly_4.10.4 remotes_2.5.0 httpuv_1.6.15
[19] glmGamPoi_1.16.0 spam_2.11-0 sessioninfo_1.2.2
[22] pkgbuild_1.4.5 spatstat.sparse_3.1-0 reticulate_1.39.0
[25] cowplot_1.1.3 pbapply_1.7-2 zlibbioc_1.50.0
[28] abind_1.4-8 pkgload_1.4.0 GenomicRanges_1.56.2
[31] Rtsne_0.17 R.utils_2.12.3 BiocGenerics_0.50.0
[34] rappdirs_0.3.3 GenomeInfoDbData_1.2.12 IRanges_2.38.1
[37] S4Vectors_0.42.1 ggrepel_0.9.6 irlba_2.3.5.1
[40] listenv_0.9.1 spatstat.utils_3.1-1 goftest_1.2-3
[43] RSpectra_0.16-2 spatstat.random_3.3-2 fitdistrplus_1.2-1
[46] parallelly_1.38.0 DelayedMatrixStats_1.26.0 DelayedArray_0.30.1
[49] leiden_0.4.3.1 codetools_0.2-20 tidyselect_1.2.1
[52] UCSC.utils_1.0.0 farver_2.1.2 matrixStats_1.4.1
[55] stats4_4.4.1 spatstat.explore_3.3-3 jsonlite_1.8.9
[58] ellipsis_0.3.2 progressr_0.15.0 iterators_1.0.14
[61] ggridges_0.5.6 survival_3.7-0 foreach_1.5.2
[64] dbscan_1.2-0 tools_4.4.1 ica_1.0-3
[67] glue_1.8.0 SparseArray_1.4.8 gridExtra_2.3
[70] MatrixGenerics_1.16.0 usethis_3.0.0 GenomeInfoDb_1.40.1
[73] withr_3.0.2 BiocManager_1.30.25 fastmap_1.2.0
[76] fansi_1.0.6 digest_0.6.37 rsvd_1.0.5
[79] timechange_0.3.0 R6_2.5.1 mime_0.12
[82] colorspace_2.1-1 scattermore_1.2 sccore_1.0.5
[85] tensor_1.5 spatstat.data_3.1-2 R.methodsS3_1.8.2
[88] utf8_1.2.4 generics_0.1.3 data.table_1.16.2
[91] S4Arrays_1.4.1 httr_1.4.7 htmlwidgets_1.6.4
[94] uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.6
[97] lmtest_0.9-40 XVector_0.44.0 SingleCellExperiment_1.26.0
[100] htmltools_0.5.8.1 profvis_0.4.0 dotCall64_1.2
[103] Biobase_2.64.0 scales_1.3.0 png_0.1-8
[106] SpatialExperiment_1.14.0 spatstat.univar_3.1-1 rstudioapi_0.17.1
[109] rjson_0.2.23 tzdb_0.4.0 reshape2_1.4.4
[112] nlme_3.1-166 cachem_1.1.0 zoo_1.8-12
[115] KernSmooth_2.23-24 parallel_4.4.1 miniUI_0.1.1.1
[118] pillar_1.9.0 grid_4.4.1 vctrs_0.6.5
[121] RANN_2.6.2 urlchecker_1.0.1 promises_1.3.0
[124] xtable_1.8-4 cluster_2.1.6 magick_2.8.5
[127] cli_3.6.3 compiler_4.4.1 rlang_1.1.4
[130] crayon_1.5.3 future.apply_1.11.3 mclust_6.1.1
[133] plyr_1.8.9 fs_1.6.5 stringi_1.8.4
[136] viridisLite_0.4.2 deldir_2.0-4 BiocParallel_1.38.0
[139] babelgene_22.9 munsell_0.5.1 lazyeval_0.2.2
[142] devtools_2.4.5 spatstat.geom_3.3-3 Matrix_1.7-1
[145] RcppHNSW_0.6.0 hms_1.1.3 sparseMatrixStats_1.16.0
[148] future_1.34.0 shiny_1.9.1 SummarizedExperiment_1.34.0
[151] ROCR_1.0-11 leidenAlg_1.1.4 igraph_2.1.1
[154] memoise_2.0.1 fastmatch_1.1-4

[vdsukhov]

@csmoreno yep it would be great if you could provide a link to the object. You can send the link to one of these email addresses: [email protected] or [email protected] (in case if it's google drive)

[csmoreno]

I found a workaround by converting from an Assay5 to an Assay class.

convert a v5 assay to a v3 assay

CM01.object[["Spatial"]] <- as(object = CM01.object[["Spatial.016um"]], Class = "Assay")

ps <- plotCoregulationProfileSpatial(Hallmark_pathways[topPathways], CM01.object, assay = "Spatial",
title=titles)

cowplot::plot_grid(plotlist=ps, ncol=2)