plotforest: plotforest: Wraps around maftools::forestPlot to more...

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

plotforest: Wraps around maftools::forestPlot to more explicitly handle pval VS fdr option and allow both to be passed while onl using the value set by bool 'threshold_on_fdr'

Description

plotforest: Wraps around maftools::forestPlot to more explicitly handle pval VS fdr option and allow both to be passed while onl using the value set by bool 'threshold_on_fdr'

Usage

plotforest(
  mafCompareRes,
  pVal = 0.05,
  fdr = 0.05,
  threshold_on_fdr,
  color = NULL,
  geneFontSize = 1.2,
  lineWidth = 2.2,
  titleSize = 1.2
)

Arguments

mafCompareRes	results from mafCompare
pVal	p-value threshold. Default 0.05.
fdr	fdr threshold. Default NULL. If provided uses adjusted pvalues (fdr).
threshold_on_fdr	should we threshold on FDR (TRUE) or on pValue (false) (flag)
color	vector of two colors for the lines. Default 'maroon' and 'royalblue'
geneFontSize	Font size for gene symbols. Default 0.8
lineWidth	line width for CI bars. Default 1
titleSize	font size for titles. Default 1.2

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