fix

R/plot_cpdb_heatmap.R

@@ -34,26 +34,26 @@
 #' @include utils.R
 #' @export
 
-plot_cpdb_heatmap <- function(
-    pvals, cell_types = NULL, degs_analysis = FALSE, log1p_transform = FALSE,
-    show_rownames = TRUE, show_colnames = TRUE, scale = "none", cluster_cols = TRUE,
-    cluster_rows = TRUE, border_color = "white", fontsize_row = 11, fontsize_col = 11,
-    family = "Arial", main = "", treeheight_col = 0, treeheight_row = 0, low_col = "dodgerblue4",
-    mid_col = "peachpuff", high_col = "deeppink4", alpha = 0.05, return_tables = FALSE,
-    symmetrical = TRUE, ...) {
+plot_cpdb_heatmap <- function(pvals, cell_types = NULL, degs_analysis = FALSE, log1p_transform = FALSE,
+  show_rownames = TRUE, show_colnames = TRUE, scale = "none", cluster_cols = TRUE,
+  cluster_rows = TRUE, border_color = "white", fontsize_row = 11, fontsize_col = 11,
+  family = "Arial", main = "", treeheight_col = 0, treeheight_row = 0, low_col = "dodgerblue4",
+  mid_col = "peachpuff", high_col = "deeppink4", alpha = 0.05, return_tables = FALSE,
+  symmetrical = TRUE, ...) {
   requireNamespace("reshape2")
   requireNamespace("grDevices")
   all_intr <- pvals
   col_start <- ifelse(colnames(all_intr)[DEFAULT_CLASS_COL] == "classification",
-    DEFAULT_V5_COL_START, DEFAULT_COL_START
-  )
+    DEFAULT_V5_COL_START, DEFAULT_COL_START)
   intr_pairs <- all_intr$interacting_pair
   all_intr <- t(all_intr[, -c(1:col_start - 1)])
   colnames(all_intr) <- intr_pairs
   if (is.null(cell_types)) {
-    cell_types <- sort(unique(unlist(strsplit(all_intr.columns[col_start:], DEFAULT_CPDB_SEP))))
+    cell_types <- sort(unique(unlist(strsplit(colnames(all_intr)[col_start:ncol(all_intr)],
+      paste0("\\", DEFAULT_CPDB_SEP)))))
   }
-  cell_types_comb <- apply(expand.grid(cell_types, cell_types), 1, function(z) paste(z, collapse = "|"))
+  cell_types_comb <- apply(expand.grid(cell_types, cell_types), 1, function(z) paste(z,
+    collapse = "|"))
   cell_types_keep <- row.names(all_intr)[row.names(all_intr) %in% cell_types_comb]
   empty_celltypes <- setdiff(cell_types_comb, cell_types_keep)
   all_intr <- all_intr[row.names(all_intr) %in% cell_types_keep, ]
@@ -95,20 +95,18 @@ plot_cpdb_heatmap <- function(
       count_mat <- log1p(count_mat)
     }
 
-    p <- pheatmap(count_mat,
-      show_rownames = show_rownames, show_colnames = show_colnames,
+    p <- pheatmap(count_mat, show_rownames = show_rownames, show_colnames = show_colnames,
       scale = scale, cluster_cols = cluster_cols, border_color = border_color,
       cluster_rows = cluster_rows, fontsize_row = fontsize_row, fontsize_col = fontsize_col,
       main = main, treeheight_row = treeheight_row, family = family, color = col.heatmap,
-      treeheight_col = treeheight_col, ...
-    )
+      treeheight_col = treeheight_col, ...)
     if (return_tables) {
       if (symmetrical) {
         all_sum <- rowSums(count_mat)
         all_sum <- data.frame(all_sum)
         return(list(count_network = count_mat, interaction_count = all_sum))
       } else {
-        count_mat <- t(count_mat) # so that the table output is the same layout as the plot
+        count_mat <- t(count_mat)  # so that the table output is the same layout as the plot
         row_sum <- rowSums(count_mat)
         col_sum <- colSums(count_mat)
         all_sum <- data.frame(row_sum, col_sum)
@@ -120,4 +118,4 @@ plot_cpdb_heatmap <- function(
   } else {
     stop("There are no significant results using p-value of: ", alpha, call. = FALSE)
   }
-}
+}