Fix main pVACview table header tooltips

Author: susannasiebert

pvactools/tools/pvacview/styling.R

@@ -10,21 +10,25 @@ rowcallback <- function(hla_count, row_num) {
 }
 
 callback <- function(hla_count, score_mode) {
+  print("HLA count")
+  print(hla_count)
   c(
     "var tips = ['Gene - The Ensembl gene name of the affected gene.',",
     "        'AA Change - The amino acid change for the mutation. Note that FS indicates a frameshift variant.',",
     "        'Num Passing Transcripts - The number of transcripts for this mutation that resulted in at least one well-binding peptide.',",
     "        'Best Peptide - The best-binding mutant epitope sequence (lowest mutant binding affinity) prioritizing epitope sequences that resulted from a protein_coding transcript with a TSL below the maximum transcript support level and having no problematic positions.',",
     "        'Best Transcript - Transcript corresponding to the best peptide with the lowest TSL and shortest length.',",
-    "        'TSL - Transcript support level of the best peptide.',",
+    "        'MANE Select - MANE select status of the best transcript.',",
+    "        'Canonical - Canonical status of the best transcript.',",
+    "        'TSL - Transcript support level of the best transcript.',",
     "        'Allele',",
     "        'Pos - The one-based position of the start of the mutation within the epitope sequence. 0 if the start of the mutation is before the epitope (as can occur downstream of frameshift mutations).',",
     "        'Prob Pos - Problematic positions within the best peptide.',",
     "        'Num Included Peptides - The number of top-scoring, unique peptides included for review.',",
     "        'Num Passing Peptides - The number of unique well-binding peptides for this mutation.',",
-    gsub("X", score_mode,"      'IC50 MT - X IC50 binding affinity of the best-binding mutant epitope across all prediction algorithms used.', "),
+    paste("      'IC50 MT -", score_mode, "IC50 binding affinity of the best-binding mutant epitope across all prediction algorithms used.', "),
     "        'IC50 WT - IC50 binding affinity of the corresponding wildtype epitope.',",
-    gsub("X", score_mode,"      '%ile MT - X binding affinity percentile rank of the best-binding mutant epitope across all prediction algorithms used (those that provide percentile output).', "),
+    paste("      '%ile MT - ", score_mode, "binding affinity percentile rank of the best-binding mutant epitope across all prediction algorithms used (those that provide percentile output).', "),
     "        '%ile WT - Binding affinity percentile rank of the corresponding wildtype epitope across all prediction algorithms used (those that provide percentile output).', ",
     "        'RNA Expr - Gene expression value for the annotated gene containing the variant.',",
     "        'RNA VAF - Tumor RNA variant allele frequency (VAF) at this position.',",
@@ -37,8 +41,8 @@ callback <- function(hla_count, score_mode) {
     "        'Rej - Click the thumbs-down button to reject a neoantigen candidate.',",
     "        'Rev - Click the flag button to mark a neoantigen candidate for review.'],",
     "header = table.columns().header();",
-    gsub("7", hla_count, "for (var i = 7; i-7 < tips.length; i++) {"),
-    gsub("7", hla_count, "$(header[i]).attr('title', tips[i-7]);"),
+    paste("for (var i = ", hla_count+1, "; i-", hla_count+1, " < tips.length; i++) {"),
+    paste("$(header[i]).attr('title', tips[i-", hla_count+1, "]);"),
     "}"
   )
 }