plotVaf {maftools} | R Documentation |
Plots vaf distribution of genes as a boxplot or violinplot.
plotVaf(maf, vafCol = NULL, genes = NULL, violin = FALSE, top = 10, orderByMedian = TRUE, flip = FALSE, fn = NULL, width = 6, height = 5)
maf |
|
vafCol |
manually specify column name for vafs. Default looks for column 't_vaf' |
genes |
specify genes for which plots has to be generated |
violin |
if TRUE plots violin plot |
top |
if |
orderByMedian |
Orders genes by decreasing median VAF. Default TRUE |
flip |
if TRUE, flips axes. Default FALSE |
fn |
Filename. If given saves plot as a output pdf. Default NULL. |
width |
Width of plot to be saved. Default 6 |
height |
Height of plot to be saved. Default 5 |
ggplot object which can be further modified.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf) plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU')