maftools (version 0.99.30)

forestPlot: Draw forest plot for differences betweeen cohorts.

Description

Draw forest plot for differences betweeen cohorts.

Usage

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

Arguments

mafCompareRes

results from mafCompare

pVal

p-value threshold. Default 0.05.

show

can be either stat or pval

color

vector of colors for cohorts. Default NULL.

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

Value

ggplot object of the plot.

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.

See Also

mafCompare

Examples

# NOT RUN {
##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')
# }