fix heatmap in mae qc for just 1 sample

gagneurlab · Apr 6, 2023 · a03a253 · a03a253
1 parent 25ad87a
commit a03a253
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/drop/modules/mae-pipeline/QC/DNA_RNA_matrix_plot.R b/drop/modules/mae-pipeline/QC/DNA_RNA_matrix_plot.R
@@ -95,9 +95,14 @@ ann_colors = list(
 ann_colors[['status']] <- ann_colors[['status']][unique(c(dna_df$status, rna_df$status))] 
 
 #+ Heatmap, fig.height=6, fig.width=8
-pheatmap(qc_mat, color = color, cluster_rows = FALSE, cluster_cols = FALSE, 
-         annotation_row = dna_df, annotation_col = rna_df, annotation_colors = ann_colors,
-         labels_row = 'DNA samples', labels_col = 'RNA samples', angle_col = 0)
+if(nrow(qc_mat) > 1 || ncol(qc_mat) > 1){
+    pheatmap(qc_mat, color = color, cluster_rows = FALSE, cluster_cols = FALSE, 
+        annotation_row = dna_df, annotation_col = rna_df, annotation_colors = ann_colors,
+        labels_row = 'DNA samples', labels_col = 'RNA samples', angle_col = 0)
+} else {
+    print("No heatmap created as only 1 sample is provided.")
+    print(qc_mat)
+}
 
 
 #' ## Identify matching samples

diff --git a/drop/modules/mae-pipeline/QC/create_matrix_dna_rna_cor.R b/drop/modules/mae-pipeline/QC/create_matrix_dna_rna_cor.R
@@ -96,7 +96,7 @@ lp <- bplapply(1:N, function(i){
 mat <- do.call(rbind, lp)
 row.names(mat) <- dna_samples
 colnames(mat) <- rna_samples
-mat <- mat[sa[rows_in_group, DNA_ID], sa[rows_in_group, RNA_ID]]
+mat <- mat[sa[rows_in_group, DNA_ID], sa[rows_in_group, RNA_ID],drop=FALSE]
 
 saveRDS(mat, snakemake@output$mat_qc)