plotmafSummary: Plots maf summary.

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Plots maf summary.

Usage

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
)

Arguments

maf	an MAF object generated by read.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.

Value

Prints plot.

See Also

read.maf MAF

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, useAll = FALSE)
plotmafSummary(maf = laml, addStat = 'median')

Example output

-Reading
-Validating
--Using only `Somatic` variants from Mutation_Status. Set useAll = TRUE to include everything.Mutation_Status not found. Assuming all variants are Somatic and validated
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.528s elapsed (0.382s cpu) 

maftools documentation built on Feb. 6, 2021, 2 a.m.