Merge pull request #300 from Sage-Bionetworks/hot-fix

Fix dashboardTemplate.Rmd panel issue
Sage-Bionetworks · May 15, 2020 · d7ca9cf · d7ca9cf
2 parents 33c5fec + 27beb3b
commit d7ca9cf
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/genie/dashboardTemplate.Rmd b/genie/dashboardTemplate.Rmd
@@ -1,9 +1,9 @@
 ---
 title: "%s Summary"
-output:
- html_document:
- toc: true
- toc_depth: 3
+output: html_document
+# html_document:
+# toc: true
+# toc_depth: 3
 params:
  genieUser:
  value: x
@@ -562,7 +562,7 @@ if (!is.null(this_bed)) {
  return(seq_assay)
  }
  })
- relevant_panels = mutated_genes[, panels_covering_tp53]
+ relevant_panels = mutated_genes[, colnames(mutated_genes) %in% panels_covering_tp53]
  relevant_panels = relevant_panels[, colnames(relevant_panels) %in% unlist(tp53_not_top)]
  top_5_mutated_genes_string = apply(relevant_panels, 2, function(x) {
  top_5 = sort(x, decreasing = T)[1:5]