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Addressing README and prettyOncoplot issues #59

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merged 4 commits into from
Mar 22, 2024
Merged

Addressing README and prettyOncoplot issues #59

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ebf3132
bug fix: inaccuracy in prettyoncoplot annoation label
Kdreval Mar 22, 2024
fb7d7d6
bug fix: ensure printout is only in verbose mode
Kdreval Mar 22, 2024
2a07dcb
cleanup: update readme
Kdreval Mar 22, 2024
9733c5e
bug fix: links in README
Kdreval Mar 22, 2024
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14 changes: 9 additions & 5 deletions R/prettyOncoplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)]))
Expand Down Expand Up @@ -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)]
Expand Down Expand Up @@ -648,12 +652,12 @@ 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",
Expand Down
13 changes: 12 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,17 @@
![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)


# 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](https://morinlab.github.io/GAMBLR.viz/)

# Contributing

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