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Updated column tooltips #1189

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Updated column tooltips #1189

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3c00d06
updated column descriptions
ldhtnp Jan 31, 2025
1dd8d02
updated additional descriptions, modified gsub
ldhtnp Feb 6, 2025
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3 changes: 2 additions & 1 deletion pvactools/tools/pvacview/styling.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ callback <- function(hla_count, score_mode) {
" '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 total number of peptides for this mutation.',",
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@susannasiebert susannasiebert Jan 31, 2025 •
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This might be a bit confusing for our users. While this does reflect the total number of peptides available in pVACview with meta-data, it's not all of the peptides resulting from the mutation. In the context of the aggregated report this is described as:

The number of included peptides according to the --aggregate-inclusion-binding-threshold and --aggregate-inclusion-count-limit

Here it might make sense to word it as "The number of top-scoring, unique peptides included for review". @malachig @chrisamiller do you have opinions on this wording.

" '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.', "),
" 'IC50 WT - IC50 binding affinity of the corresponding wildtype epitope.',",
Expand All @@ -31,7 +32,7 @@ callback <- function(hla_count, score_mode) {
" 'RNA Depth - Tumor RNA depth at this position.',",
" 'DNA VAF - Tumor DNA variant allele frequency (VAF) at this position.',",
" 'Tier - A tier suggesting the suitability of variants for use in vaccines.',",
" 'Eval - User-selected evaluation of neoantigen candidate. Options include: Accept, Reject, Review. (Default: Pending)'],",
" 'Ref Match - Indicates if the query sequence has a hit in the reference proteome.'],",
"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]);"),
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I'm not 100% sure whether the numbers here need adjusting. I think it has something to do with columns we drop for display purposes but I'm not 100% sure. If you haven't run pVACview with your modifications, please do to ensure that there are no errors or warnings related to this.

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The hla_count is now 5, so I updated the gsub commands to reflect this. I did notice when you click on a column value errors appear in the console. This occurred before and after I modified the gsub commands and also happens on the staging branch. Might be worth looking into

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I tried this change with a couple of different files and it looks like it now only works for files where the HLA count is the same as for the HCC1395 demo data. For anything with fewer or more HLAs the tooltips are shifted. If I change it back to how it was originally, it seems to work fine aside from the messages you noticed in the console. I think those are unrelated.

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