Hello,
I am encountering an error when running netVisual_diffInteraction on a merged CellChat object consisting of two datasets (wt and lysm). Both individual objects were processed using the standard CellChat pipeline (up to aggregateNet) before merging.
> setwd("V:/Tower Lab/Achira Ultron/BT scRNA 2025/cellchat")
>
> options(future.globals.maxSize = 2000 * 1024^2)
>
> library(Seurat)
> library(tidyverse)
> library(ggplot2)
> library(CellChat)
> library(patchwork)
> library(presto)
> library(future)
> library(NMF)
> library(ggalluvial)
> library(cowplot)
> library(svglite)
> library(stringr)
> library(plyr)
> library(RColorBrewer)
>
> #read all the cellchat objects
> wt <- readRDS("V:/Tower Lab/Achira Ultron/BT scRNA 2025/cellchat/cellchat_wt1.rds")
> lysm <- readRDS("V:/Tower Lab/Achira Ultron/BT scRNA 2025/cellchat/cellchat_lysm1.rds")
> levels(lysm@idents)
[1] "Stem Progenitors Cells" "Macrophages" "Neutrophils" "Monocytes" "Dendritic Cells" "T and NK Cells"
[7] "Muscle Cells" "Smooth Muscle Cells" "Osteoclasts" "Endothelial Cells" "Fibroblasts Cells"
> levels(wt@idents)
[1] "Stem Progenitors Cells" "Macrophages" "Neutrophils" "Monocytes" "Dendritic Cells" "T and NK Cells"
[7] "Fibroblasts Cells" "Muscle Cells" "Smooth Muscle Cells" "Osteoclasts" "Endothelial Cells"
> common.levels <- levels(wt@idents)
> lysm@idents <- factor(lysm@idents, levels = common.levels)
> levels(lysm@idents)
[1] "Stem Progenitors Cells" "Macrophages" "Neutrophils" "Monocytes" "Dendritic Cells" "T and NK Cells"
[7] "Fibroblasts Cells" "Muscle Cells" "Smooth Muscle Cells" "Osteoclasts" "Endothelial Cells"
> levels(wt@idents)
[1] "Stem Progenitors Cells" "Macrophages" "Neutrophils" "Monocytes" "Dendritic Cells" "T and NK Cells"
[7] "Fibroblasts Cells" "Muscle Cells" "Smooth Muscle Cells" "Osteoclasts" "Endothelial Cells"
> object.list <- list(wt = wt, lysm = lysm)
> cellchat <- mergeCellChat(object.list, add.names = names(object.list))
> View(object.list)
> cellchat <- mergeCellChat, object.list, add.names = names(object.list), cell.prefix = TRUE)
> ptm = Sys.time()
> gg1 <- compareInteractions(cellchat, show.legend = F, group = c(1,2))
> gg2 <- compareInteractions(cellchat, show.legend = F, group = c(1,2), measure = "weight")
> gg1 + gg2
**> par(mfrow = c(1,2), xpd=TRUE)
> netVisual_diffInteraction(cellchat, weight.scale = T)
Error in p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] :
replacement has length zero
> netVisual_diffInteraction(cellchat, weight.scale = T, measure = "weight")
Error in p[[type]][[name]][is.na(p[[type]][[name]])] <- i.default.values[[type]][[name]] :
replacement has length zero**
> sessionInfo()
R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] future_1.70.0 presto_1.0.0 data.table_1.18.2.1 Rcpp_1.1.1 ggalluvial_0.12.6 RColorBrewer_1.1-3 plyr_1.8.9
[8] svglite_2.2.2 cowplot_1.2.0 ComplexHeatmap_2.26.1 NMF_0.28 cluster_2.1.8.1 rngtools_1.5.2 registry_0.5-1
[15] patchwork_1.3.2 CellChat_1.6.1 Biobase_2.70.0 BiocGenerics_0.56.0 generics_0.1.4 igraph_2.2.2 lubridate_1.9.5
[22] forcats_1.0.1 stringr_1.6.0 dplyr_1.2.0 purrr_1.2.1 readr_2.2.0 tidyr_1.3.2 tibble_3.3.1
[29] ggplot2_4.0.2 tidyverse_2.0.0 Seurat_5.4.0 SeuratObject_5.3.0 sp_2.2-1
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.23 splines_4.5.2 later_1.4.8 polyclip_1.10-7 ggnetwork_0.5.14 fastDummies_1.7.5
[7] lifecycle_1.0.5 rstatix_0.7.3 doParallel_1.0.17 globals_0.19.1 lattice_0.22-7 MASS_7.3-65
[13] backports_1.5.0 magrittr_2.0.4 plotly_4.12.0 httpuv_1.6.16 otel_0.2.0 sctransform_0.4.3
[19] spam_2.11-3 spatstat.sparse_3.1-0 reticulate_1.45.0 pbapply_1.7-4 abind_1.4-8 Rtsne_0.17
[25] circlize_0.4.17 IRanges_2.44.0 S4Vectors_0.48.0 ggrepel_0.9.7 irlba_2.3.7 listenv_0.10.1
[31] spatstat.utils_3.2-2 goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.4-4 fitdistrplus_1.2-6 parallelly_1.46.1
[37] codetools_0.2-20 tidyselect_1.2.1 shape_1.4.6.1 farver_2.1.2 matrixStats_1.5.0 stats4_4.5.2
[43] spatstat.explore_3.7-0 jsonlite_2.0.0 GetoptLong_1.1.0 BiocNeighbors_2.4.0 progressr_0.18.0 Formula_1.2-5
[49] ggridges_0.5.7 survival_3.8-3 iterators_1.0.14 systemfonts_1.3.2 foreach_1.5.2 tools_4.5.2
[55] sna_2.8 ica_1.0-3 glue_1.8.0 gridExtra_2.3 withr_3.0.2 BiocManager_1.30.27
[61] fastmap_1.2.0 digest_0.6.39 timechange_0.4.0 R6_2.6.1 mime_0.13 textshaping_1.0.5
[67] colorspace_2.1-2 scattermore_1.2 tensor_1.5.1 spatstat.data_3.1-9 FNN_1.1.4.1 httr_1.4.8
[73] htmlwidgets_1.6.4 uwot_0.2.4 pkgconfig_2.0.3 gtable_0.3.6 lmtest_0.9-40 S7_0.2.1
[79] htmltools_0.5.9 carData_3.0-6 dotCall64_1.2 clue_0.3-68 scales_1.4.0 png_0.1-8
[85] spatstat.univar_3.1-6 rstudioapi_0.18.0 tzdb_0.5.0 reshape2_1.4.5 rjson_0.2.23 coda_0.19-4.1
[91] statnet.common_4.13.0 nlme_3.1-168 zoo_1.8-15 GlobalOptions_0.1.3 KernSmooth_2.23-26 parallel_4.5.2
[97] miniUI_0.1.2 pillar_1.11.1 vctrs_0.7.1 RANN_2.6.2 promises_1.5.0 ggpubr_0.6.3
[103] car_3.1-5 xtable_1.8-8 cli_3.6.5 compiler_4.5.2 rlang_1.1.7 crayon_1.5.3
[109] future.apply_1.20.2 ggsignif_0.6.4 labeling_0.4.3 stringi_1.8.7 viridisLite_0.4.3 network_1.20.0
[115] deldir_2.0-4 gridBase_0.4-7 lazyeval_0.2.2 spatstat.geom_3.7-0 Matrix_1.7-4 RcppHNSW_0.6.0
[121] hms_1.1.4 shiny_1.13.0 ROCR_1.0-12 broom_1.0.12
Hello,
I am encountering an error when running netVisual_diffInteraction on a merged CellChat object consisting of two datasets (wt and lysm). Both individual objects were processed using the standard CellChat pipeline (up to aggregateNet) before merging.
> sessionInfo()
R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] future_1.70.0 presto_1.0.0 data.table_1.18.2.1 Rcpp_1.1.1 ggalluvial_0.12.6 RColorBrewer_1.1-3 plyr_1.8.9
[8] svglite_2.2.2 cowplot_1.2.0 ComplexHeatmap_2.26.1 NMF_0.28 cluster_2.1.8.1 rngtools_1.5.2 registry_0.5-1
[15] patchwork_1.3.2 CellChat_1.6.1 Biobase_2.70.0 BiocGenerics_0.56.0 generics_0.1.4 igraph_2.2.2 lubridate_1.9.5
[22] forcats_1.0.1 stringr_1.6.0 dplyr_1.2.0 purrr_1.2.1 readr_2.2.0 tidyr_1.3.2 tibble_3.3.1
[29] ggplot2_4.0.2 tidyverse_2.0.0 Seurat_5.4.0 SeuratObject_5.3.0 sp_2.2-1
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.23 splines_4.5.2 later_1.4.8 polyclip_1.10-7 ggnetwork_0.5.14 fastDummies_1.7.5
[7] lifecycle_1.0.5 rstatix_0.7.3 doParallel_1.0.17 globals_0.19.1 lattice_0.22-7 MASS_7.3-65
[13] backports_1.5.0 magrittr_2.0.4 plotly_4.12.0 httpuv_1.6.16 otel_0.2.0 sctransform_0.4.3
[19] spam_2.11-3 spatstat.sparse_3.1-0 reticulate_1.45.0 pbapply_1.7-4 abind_1.4-8 Rtsne_0.17
[25] circlize_0.4.17 IRanges_2.44.0 S4Vectors_0.48.0 ggrepel_0.9.7 irlba_2.3.7 listenv_0.10.1
[31] spatstat.utils_3.2-2 goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.4-4 fitdistrplus_1.2-6 parallelly_1.46.1
[37] codetools_0.2-20 tidyselect_1.2.1 shape_1.4.6.1 farver_2.1.2 matrixStats_1.5.0 stats4_4.5.2
[43] spatstat.explore_3.7-0 jsonlite_2.0.0 GetoptLong_1.1.0 BiocNeighbors_2.4.0 progressr_0.18.0 Formula_1.2-5
[49] ggridges_0.5.7 survival_3.8-3 iterators_1.0.14 systemfonts_1.3.2 foreach_1.5.2 tools_4.5.2
[55] sna_2.8 ica_1.0-3 glue_1.8.0 gridExtra_2.3 withr_3.0.2 BiocManager_1.30.27
[61] fastmap_1.2.0 digest_0.6.39 timechange_0.4.0 R6_2.6.1 mime_0.13 textshaping_1.0.5
[67] colorspace_2.1-2 scattermore_1.2 tensor_1.5.1 spatstat.data_3.1-9 FNN_1.1.4.1 httr_1.4.8
[73] htmlwidgets_1.6.4 uwot_0.2.4 pkgconfig_2.0.3 gtable_0.3.6 lmtest_0.9-40 S7_0.2.1
[79] htmltools_0.5.9 carData_3.0-6 dotCall64_1.2 clue_0.3-68 scales_1.4.0 png_0.1-8
[85] spatstat.univar_3.1-6 rstudioapi_0.18.0 tzdb_0.5.0 reshape2_1.4.5 rjson_0.2.23 coda_0.19-4.1
[91] statnet.common_4.13.0 nlme_3.1-168 zoo_1.8-15 GlobalOptions_0.1.3 KernSmooth_2.23-26 parallel_4.5.2
[97] miniUI_0.1.2 pillar_1.11.1 vctrs_0.7.1 RANN_2.6.2 promises_1.5.0 ggpubr_0.6.3
[103] car_3.1-5 xtable_1.8-8 cli_3.6.5 compiler_4.5.2 rlang_1.1.7 crayon_1.5.3
[109] future.apply_1.20.2 ggsignif_0.6.4 labeling_0.4.3 stringi_1.8.7 viridisLite_0.4.3 network_1.20.0
[115] deldir_2.0-4 gridBase_0.4-7 lazyeval_0.2.2 spatstat.geom_3.7-0 Matrix_1.7-4 RcppHNSW_0.6.0
[121] hms_1.1.4 shiny_1.13.0 ROCR_1.0-12 broom_1.0.12