jinworks
Error subsetCellChat
Hi!
Thanks a lot for the great method.
I have a problem with subsetCellChat. It works well on a merged CellChat object. However if I want to apply it to a single CellChat object I get this error:
cellchat_stim_subset <- subsetCellChat(cellchat_stim, idents.use = c('B-cells_perfused','B-cells_unperfused','Endothelial cells_perfused','Monocytes_perfused','Monocytes_unperfused','NK cells_perfused','NK cells_unperfused','T-cells_perfused','T-cells_unperfused')) Error in nrow([email protected]) : no slot of name "data.smooth" for this object of class "CellChat"
Could you help me what might be the problem? Thanks a lot! Alina
sessionInfo() R version 4.4.1 (2024-06-14) Platform: x86_64-pc-linux-gnu Running under: Rocky Linux 8.8 (Green Obsidian)
Matrix products: default BLAS/LAPACK: FlexiBLAS OPENBLAS; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
[9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8
time zone: Europe/Berlin tzcode source: system (glibc)
attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DIALOGUE_1.0 UpSetR_1.4.0 beanplot_1.3.1 Hmisc_5.1-3
[5] ppcor_1.1 MASS_7.3-61 reshape2_1.4.4 unikn_1.0.0
[9] stringi_1.8.4 psych_2.4.3 plyr_1.8.9 PMA_1.2-3
[13] lmerTest_3.1-3 lme4_1.1-35.4 Matrix_1.7-0 VennDiagram_1.7.3
[17] futile.logger_1.4.3 cowplot_1.1.3 nichenetr_2.2.0 liana_0.1.14
[21] gridExtra_2.3 limma_3.60.3 CellChat_2.1.2 igraph_2.0.3
[25] DropletUtils_1.24.0 scales_1.3.0 PCDimension_1.1.13 ClassDiscovery_3.4.5
[29] oompaBase_3.2.9 cluster_2.1.6 batchelor_1.20.0 msigdbr_7.5.1
[33] bluster_1.14.0 scDblFinder_1.18.0 scran_1.32.0 umap_0.2.10.0
[37] reticulate_1.38.0 Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4
[41] ggsci_3.2.0 scater_1.32.0 scuttle_1.14.0 circlize_0.4.16
[45] ComplexHeatmap_2.20.0 writexl_1.5.0 enrichplot_1.24.0 GOSemSim_2.30.0
[49] org.Hs.eg.db_3.19.1 AnnotationDbi_1.66.0 clusterProfiler_4.12.0 gridtext_0.1.5
[53] xlsx_0.6.5 pheatmap_1.0.12 RColorBrewer_1.1-3 readxl_1.4.3
[57] rstatix_0.7.2 ggpubr_0.6.0 ResidualMatrix_1.14.0 lubridate_1.9.3
[61] forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.5
[65] tibble_3.2.1 tidyverse_2.0.0 ggrepel_0.9.5 data.table_1.15.4
[69] MAST_1.30.0 DESeq2_1.44.0 ttservice_0.4.1 tidyr_1.3.1
[73] tidySingleCellExperiment_1.14.0 ggplot2_3.5.1 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0
[77] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 IRanges_2.38.0 S4Vectors_0.42.0
[81] MatrixGenerics_1.16.0 matrixStats_1.3.0 dplyr_1.1.4 glmGamPoi_1.16.0
[85] BiocManager_1.30.23 bigmemory_4.6.4 Biobase_2.64.0 BiocGenerics_0.50.0
I too face the same issue. Please let me know, how did you resolve the issue ?
Hello. Run into the same issue. Would appreciate if anyone knows how to solve it! Thanks.
