Fix what groupings of references the subclustering is done on.

Updated expectations of the internally stored clustering information when plotting references to allow for results obtained with version between ~1.3 and this one to be plotted.
whtns · Dec 4, 2020 · 77a46c1 · 77a46c1
1 parent 41455ea
commit 77a46c1
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Showing 3 changed files with 18 additions and 18 deletions.
diff --git a/R/inferCNV_heatmap.R b/R/inferCNV_heatmap.R
@@ -969,7 +969,12 @@ plot_cnv <- function(infercnv_obj,
     # order so the current groups are shown and seperated.
 
     ordered_names <- c()
-    if (all(name_ref_groups %in% infercnv_obj@tumor_subclusters$subclusters) || !is.null(infercnv_obj@tumor_subclusters$hc[["all_references"]])) { 
+    if (!is.null(infercnv_obj@tumor_subclusters$hc[["all_references"]])) {  # this allows runs made with some versions of infercnv to be plotted, but shouldn't be happening anymore
+        ordered_names <- infercnv_obj@tumor_subclusters$hc[["all_references"]]$labels[infercnv_obj@tumor_subclusters$hc[["all_references"]]$order]
+        split_groups <- rep(1, length(ordered_names))
+        ref_data <- ref_data[, ordered_names, drop=FALSE]
+    }
+    else if (all(name_ref_groups %in% infercnv_obj@tumor_subclusters$subclusters)) { 
         if (cluster_references) {
             split_groups <- c()
             for (i in seq_along(name_ref_groups)) {
@@ -992,11 +997,6 @@ plot_cnv <- function(infercnv_obj,
                 }
             }
         }
-        else {
-            ordered_names <- infercnv_obj@tumor_subclusters$hc[["all_references"]]$labels[infercnv_obj@tumor_subclusters$hc[["all_references"]]$order]
-            split_groups <- rep(1, length(ordered_names))
-        }
-
         ref_data <- ref_data[, ordered_names, drop=FALSE]
     }
     else {

diff --git a/R/inferCNV_tumor_subclusters.R b/R/inferCNV_tumor_subclusters.R
@@ -17,12 +17,12 @@ define_signif_tumor_subclusters <- function(infercnv_obj, p_val, hclust_method,
         tumor_groups <- c(infercnv_obj@observation_grouped_cell_indices, infercnv_obj@reference_grouped_cell_indices)
     }
     else {
-        if(length(infercnv_obj@reference_grouped_cell_indices) > 0) {
-            tumor_groups <- list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE), all_references=unlist(infercnv_obj@reference_grouped_cell_indices, use.names=FALSE))
-        }
-        else {
-            tumor_groups <- list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE))
-        }
+        # if(length(infercnv_obj@reference_grouped_cell_indices) > 0) {
+        tumor_groups <- c(list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE)), infercnv_obj@reference_grouped_cell_indices)
+        # }c
+        # else {
+        #     tumor_groups <- list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE))
+        # }
     }
 
     for (tumor_group in names(tumor_groups)) {

diff --git a/R/inferCNV_tumor_subclusters.random_smoothed_trees.R b/R/inferCNV_tumor_subclusters.random_smoothed_trees.R
@@ -20,12 +20,12 @@ define_signif_tumor_subclusters_via_random_smooothed_trees <- function(infercnv_
         tumor_groups <- c(infercnv_obj@observation_grouped_cell_indices, infercnv_obj@reference_grouped_cell_indices)
     }
     else {
-        if(length(infercnv_obj@reference_grouped_cell_indices) > 0) {
-            tumor_groups <- list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE), all_references=unlist(infercnv_obj@reference_grouped_cell_indices, use.names=FALSE))
-        }
-        else {
-            tumor_groups <- list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE))
-        }
+        # if(length(infercnv_obj@reference_grouped_cell_indices) > 0) {
+        tumor_groups <- c(list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE)), infercnv_obj@reference_grouped_cell_indices)
+        # }
+        # else {
+        #     tumor_groups <- list(all_observations=unlist(infercnv_obj@observation_grouped_cell_indices, use.names=FALSE))
+        # }
     }
 
     res = list()