From 3c00d067116f12daf9a6bbff822eb1b94e98e623 Mon Sep 17 00:00:00 2001 From: ldhtnp Date: Fri, 31 Jan 2025 10:28:06 -0600 Subject: [PATCH 1/2] updated column descriptions --- pvactools/tools/pvacview/styling.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pvactools/tools/pvacview/styling.R b/pvactools/tools/pvacview/styling.R index cb228c9a..43e75fb8 100644 --- a/pvactools/tools/pvacview/styling.R +++ b/pvactools/tools/pvacview/styling.R @@ -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.',", " '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.',", @@ -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]);"), From 1dd8d02e48cc4144209342e4e0466a910a294a81 Mon Sep 17 00:00:00 2001 From: ldhtnp Date: Thu, 6 Feb 2025 07:13:35 -0600 Subject: [PATCH 2/2] updated additional descriptions, modified gsub --- pvactools/tools/pvacview/styling.R | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/pvactools/tools/pvacview/styling.R b/pvactools/tools/pvacview/styling.R index 43e75fb8..05a51279 100644 --- a/pvactools/tools/pvacview/styling.R +++ b/pvactools/tools/pvacview/styling.R @@ -20,7 +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.',", + " '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.', "), " 'IC50 WT - IC50 binding affinity of the corresponding wildtype epitope.',", @@ -32,10 +32,13 @@ 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.',", - " 'Ref Match - Indicates if the query sequence has a hit in the reference proteome.'],", + " 'Ref Match - Indicates if the query sequence has a hit in the reference proteome.',", + " 'Acpt - Click the thumbs-up button to accept a neoantigen candidate.',", + " '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]);"), + gsub("7", hla_count, "for (var i = 5; i-5 < tips.length; i++) {"), + gsub("7", hla_count, "$(header[i]).attr('title', tips[i-5]);"), "}" ) }