bugfix impacting multipatient view cell orderings

Former-commit-id: 4a395d9
Former-commit-id: b583805

R/inferCNV_heatmap.R

@@ -145,7 +145,8 @@ plot_cnv <- function(infercnv_obj,
 
  # Row separation based on reference
  ref_idx <- unlist(infercnv_obj@reference_grouped_cell_indices)
-
+ ref_idx = ref_idx[order(ref_idx)]
+
  # Column seperation by contig and label axes with only one instance of name
  contig_tbl <- table(contigs)[unique_contigs]
  col_sep <- cumsum(contig_tbl)
@@ -176,13 +177,14 @@ plot_cnv <- function(infercnv_obj,
  counter <- counter + 1
  }
  # restrict to just the obs indices
- obs_annotations_groups <- obs_annotations_groups[ unlist(obs_index_groupings) ]
-
 
+ obs_annotations_groups <- obs_annotations_groups[-ref_idx]
+
  grouping_key_coln[1] <- floor(123/(max(nchar(obs_annotations_names)) + 4)) ## 123 is the max width in number of characters, 4 is the space taken by the color box itself and the spacing around it
  if (grouping_key_coln[1] < 1) {
  grouping_key_coln[1] <- 1
  }
+
  name_ref_groups = names(infercnv_obj@reference_grouped_cell_indices)
  grouping_key_coln[2] <- floor(123/(max(nchar(name_ref_groups)) + 4)) ## 123 is the max width in number of characters, 4 is the space taken by the color box itself and the spacing around it
  if (grouping_key_coln[2] < 1) {
@@ -195,7 +197,7 @@ plot_cnv <- function(infercnv_obj,
  # Calculate how much bigger the output needs to be to accodomate for the grouping key
  grouping_key_height <- c((grouping_key_rown[2] + 2) * 0.175, (grouping_key_rown[1] + 3) * 0.175)
 
-  # Rows observations, Columns CHR
+ # Rows observations, Columns CHR
  if (! is.na(output_format)) {
  if (output_format == "pdf") {
  pdf(paste(out_dir, paste(output_filename, ".pdf", sep=""), sep="/"),
@@ -219,7 +221,7 @@ plot_cnv <- function(infercnv_obj,
  ## They are more informative anyway
  obs_data <- infercnv_obj@expr.data
  if (!is.null(ref_idx)){
- obs_data <- plot_data[, -1 * ref_idx, drop=FALSE]
+ obs_data <- plot_data[, -ref_idx, drop=FALSE]
  if (ncol(obs_data) == 1) {
  # hack for dealing with single entries
  plot_data <- cbind(obs_data, obs_data)
@@ -244,7 +246,7 @@ plot_cnv <- function(infercnv_obj,
  current_grp_idx <- current_grp_idx + 1
  }
  ref_groups <- updated_ref_groups
-
+ 
  nb_breaks <- 16
  breaksList_t <-
  seq(min(min(obs_data_t, na.rm=TRUE), min(ref_data_t, na.rm=TRUE)),