maftools_plot_rainfall: Maftools rainfallPlot Wrapper

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

Maftools rainfallPlot Wrapper

Description

Wraps maftools::rainfallPlot. The original function plots a rainfall graph, prints the predicted kataegis coords as a df, and writes it to a file. This function does all of this EXCEPT it hides the printed df, reads the df from the file and returns it. It also deletes the created file.

Usage

maftools_plot_rainfall(
  maf,
  tsb,
  detectChangePoints = TRUE,
  ref.build = "hg19",
  pointSize = 0.4,
  fontSize = 1.2
)

Arguments

maf	an MAF object generated by read.maf. Required.
tsb	specify sample names (Tumor_Sample_Barcodes) (string)
detectChangePoints	If TRUE, detectes genomic change points where potential kataegis are formed. Results are written to an output tab delimted file.
ref.build	Reference build for chromosome sizes. Can be hg18, hg19 or hg38. Default hg19.
pointSize	Default 0.8.
fontSize	Default 12.

Value

predicted kataegis sites (dataframe)

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.