plotmafSummary {maftools} | R Documentation |
Plots maf summary.
plotmafSummary(maf, file = NULL, rmOutlier = TRUE, dashboard = TRUE, titvRaw = TRUE, width = 10, height = 7, addStat = NULL, showBarcodes = FALSE, fs = 10, textSize = 2, color = NULL, statFontSize = 3, titleSize = c(10, 8), titvColor = NULL, top = 10)
maf |
|
file |
If given pdf file will be generated. |
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. |
width |
plot parameter for output file. |
height |
plot parameter for output file. |
addStat |
Can be either mean or median. Default NULL. |
showBarcodes |
include sample names in the top bar plot. |
fs |
base size for text. Default 10. |
textSize |
font size if showBarcodes is TRUE. Default 2. |
color |
named vector of colors for each Variant_Classification. |
statFontSize |
font size if addStat is used. Default 3. |
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')