From ebf3132df5b2f6fe924d6b69207be31c0f7c9c55 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Thu, 21 Mar 2024 22:15:32 -0700 Subject: [PATCH 1/4] bug fix: inaccuracy in prettyoncoplot annoation label --- R/prettyOncoplot.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R index a353084..751c29c 100644 --- a/R/prettyOncoplot.R +++ b/R/prettyOncoplot.R @@ -648,12 +648,12 @@ prettyOncoplot = function(maf_df, is.na(estimate) ~ "NA", estimate<=1 & q.value <= 0.1 ~ these_comparisons[2], estimate > 1 & q.value <= 0.1 ~ these_comparisons[1], - TRUE ~ "Both" + TRUE ~ "Neither" )) %>% pull("Enriched in") right_annotation = rowAnnotation(" " = enrichment_label, - col = list(" " = c(GAMBLR.helpers::get_gambl_colours()[these_comparisons], Both = "#ACADAF", "NA" = "#000000")), + col = list(" " = c(GAMBLR.helpers::get_gambl_colours()[these_comparisons], Neither = "#ACADAF", "NA" = "#000000")), simple_anno_size = unit(metadataBarHeight, "mm"), annotation_legend_param = list(title = "Enriched in", From fb7d7d62eeb9d2cddb42f8422e254fb4c46aa011 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Thu, 21 Mar 2024 22:18:11 -0700 Subject: [PATCH 2/4] bug fix: ensure printout is only in verbose mode --- R/prettyOncoplot.R | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/R/prettyOncoplot.R b/R/prettyOncoplot.R index 751c29c..6c08681 100644 --- a/R/prettyOncoplot.R +++ b/R/prettyOncoplot.R @@ -200,7 +200,9 @@ prettyOncoplot = function(maf_df, group_by(Tumor_Sample_Barcode) %>% summarize(total = n(), .groups = "drop") %>% arrange(desc(total)) %>% pull(Tumor_Sample_Barcode) - print(paste("numcases:", length(tsbs))) + if(verbose){ + print(paste("numcases:", length(tsbs))) + } if(!removeNonMutated){ tsb.include = matrix(data = 0, nrow = nrow(mat_origin), ncol = length(tsbs[!tsbs %in% colnames(mat_origin)])) @@ -238,8 +240,10 @@ prettyOncoplot = function(maf_df, group_by(Tumor_Sample_Barcode) %>% summarize(total = n(), .groups = "drop") %>% arrange(desc(total)) %>% pull(Tumor_Sample_Barcode) - print(paste("numcases:",length(tsbs))) - print(paste("numgenes:",length(mat_origin[,1]))) + if(verbose){ + print(paste("numcases:",length(tsbs))) + print(paste("numgenes:",length(mat_origin[,1]))) + } if(!removeNonMutated){ tsb.include = matrix(data = 0, nrow = nrow(mat_origin), ncol = length(tsbs[!tsbs %in% colnames(mat_origin)])) colnames(tsb.include) = tsbs[!tsbs %in% colnames(mat_origin)] From 2a07dcbbf23a51d4f9fb0d1ba848792ae050616d Mon Sep 17 00:00:00 2001 From: Kdreval Date: Thu, 21 Mar 2024 22:32:30 -0700 Subject: [PATCH 3/4] cleanup: update readme --- README.md | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ebef2b1..6fa0311 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,17 @@ +[![Build check](https://github.com/morinlab/GAMBLR.viz/actions/workflows/badge.svg)](https://github.com/morinlab/GAMBLR.viz/actions) +![GitHub R package version](https://img.shields.io/github/r-package/v/morinlab/GAMBLR.viz) +![GitHub commit activity](https://img.shields.io/github/commit-activity/m/morinlab/GAMBLR.viz) +![GitHub last commit](https://img.shields.io/github/last-commit/morinlab/GAMBLR.viz) + + # GAMBLR.viz -Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R +Collection of functions to make plots for Genomic Analysis of Mature B-cell +Lymphomas in R. + +For detailed information about how to install, bundled resources, functionality +overview, tutorials, frequently asked questions and much more please visit the +website [morinlab.github.io/GAMBLR.viz](morinlab.github.io/GAMBLR.viz) # Contributing From 9733c5e76729c316c46ce13ab0c4f2908879db03 Mon Sep 17 00:00:00 2001 From: Kdreval Date: Thu, 21 Mar 2024 22:35:55 -0700 Subject: [PATCH 4/4] bug fix: links in README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 6fa0311..86c6fb0 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build check](https://github.com/morinlab/GAMBLR.viz/actions/workflows/badge.svg)](https://github.com/morinlab/GAMBLR.viz/actions) +![Build check](https://github.com/morinlab/GAMBLR.viz/actions/workflows/build_check.yaml/badge.svg) ![GitHub R package version](https://img.shields.io/github/r-package/v/morinlab/GAMBLR.viz) ![GitHub commit activity](https://img.shields.io/github/commit-activity/m/morinlab/GAMBLR.viz) ![GitHub last commit](https://img.shields.io/github/last-commit/morinlab/GAMBLR.viz) @@ -11,7 +11,7 @@ Lymphomas in R. For detailed information about how to install, bundled resources, functionality overview, tutorials, frequently asked questions and much more please visit the -website [morinlab.github.io/GAMBLR.viz](morinlab.github.io/GAMBLR.viz) +website [morinlab.github.io/GAMBLR.viz](https://morinlab.github.io/GAMBLR.viz/) # Contributing