ERROR in `netAnalysis_signalingRole_heatmap()`: Error in outgoing[, i] <- centr[[i]][[x.measure]]

Hi all!

I've used CellChat the previous month for an important experiment that needed some revisiting now. While looking at the update I wanted to use some of the new functions available to obtain a general overview of the pathways being "communicated" within my experiment.

In my experiment I have three different conditions that I store in CellChat objects like so (from scratch. not updating previous objects):

seurat <- readRDS('/local/mmoradiellos/work_stuff/post-TFM/breast.cancer_single_cell_collaboration/1_cellchat_work_per_se/input/seurat_new_annotation.RDS')

  experiment_conditions <- SplitObject(seurat, split.by = 'hypoxia_label') # Split by control, low-hypoxia or high-hypoxia
  names(experiment_conditions) <- c('control', 'high_hypoxia', 'low_hypoxia')
  experiment_conditions <- experiment_conditions[c(1,3,2)] # Reorder to have the timeline right

  # Data initialization and CellChat object creation separately per experiment condition
  cellchat_breast <- setNames(lapply(names(experiment_conditions), function(condition) { 
    data.input <- GetAssayData(experiment_conditions[[condition]], assay = 'RNA', slot = 'data') # Normalized data matrix
    labels <- Idents(experiment_conditions[[condition]]) # Cell types defined from Seurat's resulting clusters
    cell_type_df <- data.frame(group = labels, row.names = names(labels)) # To identify the different cell clusters

    cellchat_cond <- createCellChat(object = data.input, meta = cell_type_df, group.by = 'group') 
    cellchat_cond <- addMeta(cellchat_cond, meta = cell_type_df, meta.name = 'group') # Add cell information
    cellchat_cond <- setIdent(cellchat_cond, ident.use = 'group') # Set "labels" as default cell identity
    cellchat_cond@DB <- CellChatDB.mouse # Import Ligand-Receptor Database on Mouse
    cellchat_cond <- subsetData(cellchat_cond) # Uses whole database to extract all signaling genes
    future::plan('multisession', workers = 4)
    cellchat_cond <- identifyOverExpressedGenes(cellchat_cond)        # Identify Genes and Ligand-Receptor interactions
    cellchat_cond <- identifyOverExpressedInteractions(cellchat_cond) # from the database and adds it to the object
    cellchat_cond <- computeCommunProb(cellchat_cond, population.size = T) # scRNAseq experiment was unsorted, uses Chromium 10x Standard Procedure
    cellchat_cond <- filterCommunication(cellchat_cond, min.cells = 10) # Filter out groups with low cell count in groups, maybe not representative 
    cellchat_cond <- computeCommunProbPathway(cellchat_cond)  # Infers probability from expression value of genes and reference database
    cellchat_cond <- aggregateNet(cellchat_cond) 
    print( data.frame('cell_type' = levels(cellchat_cond@idents) , 'group' = as.numeric(table(cellchat_cond@idents))) ) # To check "composition" differences
    return(cellchat_cond) 
  }), names(experiment_conditions) )
  saveRDS(cellchat_breast, file = 'cellchat/cellchat_outputs/cellchat_object.cellclustersize_filtered.pop_size_F.RDS')

Next I follow the new part of the vignette (specifically Part IV) but whenever I want to use any of the functions on one of my experimental conditions-specific object I get an error:

cellchat_breast$low_hypoxia <- netAnalysis_computeCentrality(cellchat_breast$low_hypoxia, slot.name = "netP")
netAnalysis_signalingRole_heatmap(cellchat_breast$low_hypoxia, pattern = "outgoing")
Error in outgoing[, i] <- centr[[i]][[x.measure]] : 
  number of items to replace is not a multiple of replacement length

I don't know exactly what I'm doing wrong and when I checked for past issues some looked pretty similar (#479 ) but their solution didn't help me or it did not seem to fit what I want to do, which is working on separate objects per experimental condition to check overall trends to later focus on.

Thanks in advance and sorry if this is a stupid question

sqjin / CellChat

ERROR in `netAnalysis_signalingRole_heatmap()`: Error in outgoing[, i] <- centr[[i]][[x.measure]] #559