Creates a set of plot summarising a maf file.
maf_viz(maf, ...)
maf | Raw maf dataframe containing alteration data |
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... | any argument belonging to the binmat method |
Returns a list of the following plots:
varclass Barplot of counts of each variant classification
vartype Barplot of counts of each variant type
snvclass Histogram of counts of each SNV class
samplevar Histogram of counts variants per patient
topgenes Barplot of counts of top variant genes
genecor Correlation heatmap of the top 10 genes
library(gnomeR) library(dplyr) library(dtplyr) patients <- as.character(unique(mut$Tumor_Sample_Barcode))[1:200] all.plots <- maf_viz(maf=mut %>% filter(Tumor_Sample_Barcode %in% patients))#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.#> Warning: All samples were sequenced on the same platform. #> The specify.plat argument has been overwritten to FALSE.