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Fix pVACview aggregate report header tooltips #1463

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susannasiebert merged 1 commit into from
Sep 16, 2026
Merged

Fix pVACview aggregate report header tooltips #1463

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21 changes: 14 additions & 7 deletions pvactools/tools/pvacview/styling.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,20 +14,27 @@ callback <- function(hla_count, score_mode) {
"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 Peptide - The best mutant epitope sequence, taking into account various criteria such as mutant binding affinity, epitopes arising from a protein_coding transcript, the MANE Select transcript, the Canonical transcript, or a transcript with TSL below the maximum transcript support level (depending on the chosen transcript prioritization strategy), no problematic positions, passes the anchor evaluation.',",
" 'Best Transcript - Transcript corresponding to the best peptide with the lowest TSL and shortest length.',",
" 'MANE Select - MANE select status of the best transcript.',",
" 'Canonical - Canonical status of the best transcript.',",
" 'TSL - Transcript support level of the best transcript.',",
" 'Transcript Pass - Reflects whether the transcript giving rise to the Best Peptide passes the transcript evaluation, i.e., the transcript is either the MANE Select transcript, the Canonical transcript or has TSL below the maximum transcript support level. Criteria to be evaluated depend on the selected transcript prioritization strategy.',",
" '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.',",
" 'Pos - A list of the mutated positions (one-based) in the Best Peptide compared to its matched wild type peptide. NA if there is no matched wild type.',",
" '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.',",
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.',",
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).', ",
paste(" 'IC50 MT - ", score_mode, "IC50 binding affinity of the Best Peptide across all binding affinity prediction algorithms used.', "),

@tmooney tmooney Sep 9, 2026

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It looks like these paste lines have a different number of leading spaces from the literal strings in this list. Is this intentional?

@susannasiebert susannasiebert Sep 9, 2026

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I tested this change locally and it runs without issue so I don't think the number of spaces matters. I believe this is mainly done for human readability (I didn't write this originally so I'm not sure). I think the original intend was to maybe align all array entries with the first entry on line 14 but that no longer seems to be the case either way.

" 'IC50 WT - IC50 binding affinity of the corresponding wild type peptide.',",
paste(" '%ile MT - ", score_mode, "combined percentile rank of the Best Peptide across all prediction algorithms used (those that provide percentile output).', "),
" '%ile WT - Combined percentile rank of the corresponding wild type epitope across all prediction algorithms used (those that provide percentile output).', ",
paste(" 'IC50 %ile MT - ", score_mode, "binding percentile rank of the Best Peptide across all binding prediction algorithms used (those that provide percentile output).', "),
" 'IC50 %ile WT - binding percentile rank of the corresponding wild type epitope across all binding prediction algorithms used (those that provide percentile output).', ",
paste(" 'Pres %ile MT - ", score_mode, "presentation percentile rank of the Best Peptide across all presentation prediction algorithms used (those that provide percentile output).', "),
" 'Pres %ile WT - presentation percentile rank of the corresponding wild type epitope across all presentation prediction algorithms used (those that provide percentile output).', ",
paste(" 'IM %ile MT - ", score_mode, "immunogenicity percentile rank of the Best Peptide across all immunogenicity prediction algorithms used (those that provide percentile output).', "),
" 'IM %ile WT - immunogenicity percentile rank of the corresponding wild type epitope across all immunogenicity 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.',",
" 'Allele Expr - Gene expression value * Tumor RNA VAF. This is used to approximate the expression of the variant allele.',",
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