plotVaf {maftools} | R Documentation |
Plots vaf distribution of genes as a boxplot.
plotVaf(maf, vafCol = NULL, genes = NULL, top = 10, orderByMedian = TRUE, keepGeneOrder = FALSE, flip = FALSE, fn = NULL, gene_fs = 0.8, axis_fs = 0.8, height = 5, width = 5, showN = TRUE)
maf |
|
vafCol |
manually specify column name for vafs. Default looks for column 't_vaf' |
genes |
specify genes for which plots has to be generated |
top |
if |
orderByMedian |
Orders genes by decreasing median VAF. Default TRUE |
keepGeneOrder |
keep gene order. Default FALSE |
flip |
if TRUE, flips axes. Default FALSE |
fn |
Filename. If given saves plot as a output pdf. Default NULL. |
gene_fs |
font size for gene names. Default 0.8 |
axis_fs |
font size for axis. Default 0.8 |
height |
Height of plot to be saved. Default 5 |
width |
Width of plot to be saved. Default 4 |
showN |
if TRUE, includes number of observations |
Nothing.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf) plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU')