Fix duplicate chunk of code following the merge of one cell group fix…

… merge.

Former-commit-id: e3f7c6e

R/inferCNV_heatmap.R

@@ -545,12 +545,12 @@ plot_cnv <- function(infercnv_obj,
 
         ## Clustering separately by groups (ie. patients)
 
-        for (i in seq(1, max(obs_annotations_groups))) {
-            gene_indices_in_group <- which(obs_annotations_groups == i)
-            num_genes_in_group <- length(gene_indices_in_group)
-            flog.info(sprintf("Number of genes in group(%d) is %d", i, num_genes_in_group))
+        for (i in seq_len(max(obs_annotations_groups))) {
+            cell_indices_in_group <- which(obs_annotations_groups == i)
+            num_cells_in_group <- length(cell_indices_in_group)
+            flog.info(sprintf("Number of cells in group(%d) is %d", i, num_cells_in_group))
 
-            if (num_genes_in_group < 2) {
+            if (num_cells_in_group < 2) {
                 flog.info(sprintf("Skipping group: %d, since less than 2 entries", i))
                 ordered_names <- c(ordered_names, row.names(obs_data[which(obs_annotations_groups == i),, drop=FALSE]))
                 dfake = list()
@@ -577,7 +577,7 @@ plot_cnv <- function(infercnv_obj,
                 }
             }
             else {
-                data_to_cluster <- obs_data[gene_indices_in_group, hcl_group_indices, drop=FALSE]
+                data_to_cluster <- obs_data[cell_indices_in_group, hcl_group_indices, drop=FALSE]
                 flog.info(paste("group size being clustered: ", paste(dim(data_to_cluster), collapse=","), sep=" "))
                 group_obs_hcl <- hclust(dist(data_to_cluster), method=hclust_method)
                 ordered_names <- c(ordered_names, row.names(obs_data[which(obs_annotations_groups == i), ])[group_obs_hcl$order])
@@ -591,13 +591,8 @@ plot_cnv <- function(infercnv_obj,
                     write.tree(as.phylo(group_obs_hcl),
                                file=paste(file_base_name, sprintf("%s.observations_dendrogram.txt", output_filename_prefix), sep=.Platform$file.sep), append=TRUE)
                 }
-
-                group_obs_dend <- as.dendrogram(group_obs_hcl)
-                obs_dendrogram[[length(obs_dendrogram) + 1]] <- group_obs_dend
-                hcl_obs_annotations_groups <- c(hcl_obs_annotations_groups, rep(i, length(which(obs_annotations_groups == i))))
             }
 
-
             group_obs_dend <- as.dendrogram(group_obs_hcl)
             obs_dendrogram[[length(obs_dendrogram) + 1]] <- group_obs_dend
             hcl_obs_annotations_groups <- c(hcl_obs_annotations_groups, rep(i, length(which(obs_annotations_groups == i))))