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))))