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morinlab / GAMBLR.viz

Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R
https://morinlab.github.io/GAMBLR.viz/
MIT License
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`heatmap_mutation_frequency_bin` shows pathology even when not specified #41

Closed kmcoyle closed 3 months ago

kmcoyle commented 5 months ago

Functionality of other viz functions returns pathology only if no metadata column is selected; this function shows pathology as metadata even if it is not specified (and other metadata is specified).

Example:

aSHM.regions.hg38 <- data.frame("chrom" = c("chr22","chr2", "chr11", "chr14"), 
                                                start = c(22026076,88857361, 69641155, 105586437) , 
                                                end = c(22922913, 90235368, 69654474, 106879844), 
                                                name = c("IGL", "IGK", "CCND1", "IGH"))

heatmap_mutation_frequency_bin(regions_bed = aSHM.regions.hg38, 
                               these_samples_metadata = get_gambl_metadata() %>% filter(pathology == "MCL"), 
                               projection="hg38", 
                               metadataColumns = c("cohort"))
kmcoyle commented 5 months ago

Related: it doesn't return samples in the matrix if specified metadata is NA .