From 64c09e5fdf30499f7e1481481eeba4c916d88686 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 9 Sep 2026 07:40:49 -0500 Subject: [PATCH] Fix pVACview aggregate report header tooltips --- pvactools/tools/pvacview/styling.R | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/pvactools/tools/pvacview/styling.R b/pvactools/tools/pvacview/styling.R index 598bbacd7..f08c70e8d 100644 --- a/pvactools/tools/pvacview/styling.R +++ b/pvactools/tools/pvacview/styling.R @@ -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.', "), + " '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.',",