Draw forest plot for differences betweeen cohorts.
Draw forest plot for differences betweeen cohorts.
forestPlot( mafCompareRes, pVal = 0.05, fdr = NULL, color = NULL, geneFontSize = 1.2, titleSize = 1.2, lineWidth = 2.2 )
mafCompareRes |
results from |
pVal |
p-value threshold. Default 0.05. |
fdr |
fdr threshold. Default NULL. If provided uses adjusted pvalues (fdr). |
color |
vector of colors for cohorts. Default NULL. |
geneFontSize |
Font size for gene symbols. Default 1.2 |
titleSize |
font size for titles. Default 1.2 |
lineWidth |
line width for CI bars. Default 2.2 |
Plots results from link{mafCompare} as a forest plot with x-axis as log10 converted odds ratio and differentially mutated genes on y-axis.
Nothing
##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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.