Fix an issue of 'netVisual_circle' when using 'sources.use'

R/visualization.R

@@ -1297,13 +1297,26 @@ netVisual_circle <-function(net, color.use = NULL,title.name = NULL, sources.use
  }
  net[is.na(net)] <- 0
 
-
+ if (is.null(color.use)) {
+ color.use = scPalette(nrow(net))
+ names(color.use) <- rownames(net)
+ } else {
+ if (is.null(names(color.use))) {
+ stop("The input `color.use` should be a named vector! \n")
+ }
+ }
  if (remove.isolate) {
  idx1 <- which(Matrix::rowSums(net) == 0)
  idx2 <- which(Matrix::colSums(net) == 0)
- idx <- intersect(idx1, idx2)
- net <- net[-idx, ]
- net <- net[, -idx]
+ idx.isolate <- intersect(idx1, idx2)
+ if (length(idx.isolate) > 0) {
+ net <- net[-idx.isolate, ]
+ net <- net[, -idx.isolate]
+ color.use = color.use[-idx.isolate]
+ if (length(unique(vertex.weight)) > 1) {
+ vertex.weight <- vertex.weight[-idx.isolate]
+ }
+ }
  }
 
  g <- graph_from_adjacency_matrix(net, mode = "directed", weighted = T)
@@ -1314,9 +1327,7 @@ netVisual_circle <-function(net, color.use = NULL,title.name = NULL, sources.use
  }else{
  coords_scale<-coords
  }
- if (is.null(color.use)) {
- color.use = scPalette(length(igraph::V(g)))
- }
+
  if (is.null(vertex.weight.max)) {
  vertex.weight.max <- max(vertex.weight)
  }
@@ -2848,8 +2859,9 @@ netVisual_chord_gene <- function(object, slot.name = "net", color.use = NULL,
  prob[pval > thresh] <- 0
  net <- reshape2::melt(prob, value.name = "prob")
  colnames(net)[1:3] <- c("source","target","interaction_name")
-
- pairLR = dplyr::select(object@LR$LRsig, c("interaction_name_2", "pathway_name", "ligand", "receptor" ,"annotation","evidence"))
+ cols.default <- c("interaction_name_2", "pathway_name", "ligand", "receptor" ,"annotation","evidence")
+ cols.common <- intersect(cols.default,colnames(object@LR$LRsig))
+ pairLR = dplyr::select(object@LR$LRsig, cols.common)
  idx <- match(net$interaction_name, rownames(pairLR))
  temp <- pairLR[idx,]
  net <- cbind(net, temp)