Plots maf summary.
Plots maf summary.
plotmafSummary( maf, rmOutlier = TRUE, dashboard = TRUE, titvRaw = TRUE, log_scale = FALSE, addStat = NULL, showBarcodes = FALSE, fs = 1, textSize = 0.8, color = NULL, titleSize = c(1, 0.8), titvColor = NULL, top = 10 )
maf |
|
rmOutlier |
If TRUE removes outlier from boxplot. |
dashboard |
If FALSE plots simple summary instead of dashboard style. |
titvRaw |
TRUE. If false instead of raw counts, plots fraction. |
log_scale |
FALSE. If TRUE log10 transforms Variant Classification, Variant Type and Variants per sample sub-plots. |
addStat |
Can be either mean or median. Default NULL. |
showBarcodes |
include sample names in the top bar plot. |
fs |
base size for text. Default 1 |
textSize |
font size if showBarcodes is TRUE. Default 0.8 |
color |
named vector of colors for each Variant_Classification. |
titleSize |
font size for title and subtitle. Default c(10, 8) |
titvColor |
colors for SNV classifications. |
top |
include top n genes dashboard plot. Default 10. |
Prints plot.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, useAll = FALSE)
plotmafSummary(maf = laml, addStat = 'median')Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.