forestPlot {maftools}R Documentation

Draw forest plot for differences betweeen cohorts.

Description

Draw forest plot for differences betweeen cohorts.

Usage

forestPlot(mafCompareRes, pVal = 0.05, fdr = NULL, show = NULL,
  color = NULL, geneFontSize = 12, file = NULL, width = 5, height = 6)

Arguments

mafCompareRes

results from mafCompare

pVal

p-value threshold. Default 0.05.

fdr

fdr threshold. Default NULL. If provided uses adjusted pvalues (fdr).

show

can be either stat or pval

color

vector of colors for cohorts. Default NULL.

geneFontSize

Font size for gene symbols. Default 12

file

basename for output file. Plot will saved to an output pdf.

width

width of plot to be generated

height

height of plot to be generated

Details

Plots results from link{mafCompare} as a forest plot with x-axis as log10 converted odds ratio and differentially mutated genes on y-axis.

Value

ggplot object of the plot.

See Also

mafCompare

Examples

##Primary and Relapse APL
primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
##Read mafs
primary.apl <- read.maf(maf = primary.apl)
relapse.apl <- read.maf(maf = relapse.apl)
##Perform analysis and draw forest plot.
pt.vs.rt <- mafCompare(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary',
m2Name = 'Relapse', minMut = 5)
forestPlot(mafCompareRes = pt.vs.rt, show = 'stat')
[Package maftools version 1.4.28 Index]