CellChat2 computeCommunProb error

[kcavagnero]

Hi Sqjin,

Thank you for the great package. v1 has been such a great resource for the single cell community. Looking forward to using v2 with the larger L-R database but I am having some issues getting started.

When running computeCommunProb() I get the below error
in if (object@options$data type != "rna") {: argument is of length zero

I suspect this is because
dim([email protected])
0,0

Previously with same data using v1 did not have this issue and
dim([email protected])
744,14891

For both versions I created my cellchat objects from seurat using the code below.

library(Seurat)
library(CellChat)
data.input <- GetAssayData(healthy, assay = "RNA", slot = "data") # normalized data matrix
Idents(healthy) <- "celltype"
labels <- Idents(healthy)
meta <- data.frame(group = labels, row.names = names(labels))
cellchat <- createCellChat(object = data.input, meta = meta, group.by = "group")

Any idea how to fix?

sessionInfo()
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: /home/kecavagn/miniconda3/envs/seurat_cellchat2/lib/libopenblasp-r0.3.20.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] patchwork_1.1.3 CellChat_2.0.0 Biobase_2.54.0
[4] BiocGenerics_0.40.0 ggplot2_3.4.4 igraph_1.5.1
[7] dplyr_1.1.4 sp_1.4-7 SeuratObject_4.1.0
[10] Seurat_4.1.1

loaded via a namespace (and not attached):
[1] backports_1.4.1 circlize_0.4.15 uuid_1.1-1
[4] systemfonts_1.0.5 NMF_0.26 plyr_1.8.9
[7] repr_1.1.4 lazyeval_0.2.2 splines_4.1.3
[10] BiocParallel_1.28.3 listenv_0.9.0 scattermore_0.8
[13] ggnetwork_0.5.12 gridBase_0.4-7 digest_0.6.33
[16] foreach_1.5.2 htmltools_0.5.7 ggalluvial_0.12.5
[19] fansi_1.0.5 magrittr_2.0.3 tensor_1.5
[22] cluster_2.1.3 doParallel_1.0.17 ROCR_1.0-11
[25] sna_2.7-1 ComplexHeatmap_2.15.4 globals_0.16.2
[28] matrixStats_1.1.0 svglite_2.1.2 spatstat.sparse_2.1-1
[31] colorspace_2.1-0 ggrepel_0.9.4 crayon_1.5.2
[34] jsonlite_1.8.7 progressr_0.10.0 spatstat.data_2.2-0
[37] survival_3.3-1 zoo_1.8-10 iterators_1.0.14
[40] glue_1.6.2 polyclip_1.10-0 registry_0.5-1
[43] gtable_0.3.4 leiden_0.4.2 GetoptLong_1.0.5
[46] car_3.1-2 shape_1.4.6 future.apply_1.11.0
[49] abind_1.4-5 scales_1.2.1 rngtools_1.5.2
[52] rstatix_0.7.2 spatstat.random_2.2-0 miniUI_0.1.1.1
[55] Rcpp_1.0.11 viridisLite_0.4.2 xtable_1.8-4
[58] clue_0.3-65 reticulate_1.34.0 spatstat.core_2.4-2
[61] stats4_4.1.3 htmlwidgets_1.6.2 httr_1.4.7
[64] FNN_1.1.3.2 RColorBrewer_1.1-3 ellipsis_0.3.2
[67] ica_1.0-2 farver_2.1.1 pkgconfig_2.0.3
[70] sass_0.4.7 uwot_0.1.11 deldir_1.0-6
[73] utf8_1.2.4 labeling_0.4.3 tidyselect_1.2.0
[76] rlang_1.1.2 reshape2_1.4.4 later_1.3.1
[79] munsell_0.5.0 tools_4.1.3 cachem_1.0.8
[82] cli_3.6.1 generics_0.1.3 statnet.common_4.9.0
[85] broom_1.0.5 ggridges_0.5.3 evaluate_0.23
[88] stringr_1.5.1 fastmap_1.1.1 goftest_1.2-3
[91] fitdistrplus_1.1-8 purrr_1.0.2 RANN_2.6.1
[94] pbapply_1.7-2 future_1.33.0 nlme_3.1-157
[97] mime_0.12 compiler_4.1.3 plotly_4.10.3
[100] png_0.1-8 ggsignif_0.6.4 spatstat.utils_2.3-1
[103] tibble_3.2.1 bslib_0.5.1 stringi_1.8.1
[106] RSpectra_0.16-1 rgeos_0.5-9 lattice_0.20-45
[109] IRdisplay_1.1 Matrix_1.6-3 vctrs_0.6.4
[112] pillar_1.9.0 lifecycle_1.0.4 BiocManager_1.30.22
[115] GlobalOptions_0.1.2 spatstat.geom_2.4-0 lmtest_0.9-40
[118] jquerylib_0.1.4 RcppAnnoy_0.0.19 BiocNeighbors_1.12.0
[121] data.table_1.14.8 cowplot_1.1.1 irlba_2.3.5.1
[124] httpuv_1.6.12 R6_2.5.1 network_1.18.1
[127] promises_1.2.1 KernSmooth_2.23-20 gridExtra_2.3
[130] IRanges_2.28.0 parallelly_1.36.0 codetools_0.2-18
[133] MASS_7.3-57 rjson_0.2.21 withr_2.5.2
[136] presto_1.0.0 sctransform_0.3.3 S4Vectors_0.32.4
[139] mgcv_1.8-40 parallel_4.1.3 grid_4.1.3
[142] rpart_4.1.16 tidyverse_2.0.0 IRkernel_1.3
[145] coda_0.19-4 tidyr_1.3.0 carData_3.0-5
[148] Cairo_1.5-15 Rtsne_0.16 ggpubr_0.6.0
[151] pbdZMQ_0.3-7 shiny_1.8.0 base64enc_0.1-3

[kcavagnero]

Update: this issue resolves when switching from
CellChatDB.use <- CellChatDB # simply use the default CellChatDB
to
CellChatDB.use <- subsetDB(CellChatDB, search = "Secreted Signaling", key = "annotation") # use Secreted Signaling