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, color = NULL,
      geneFontSize = 1.2, titleSize = 1.2, lineWidth = 2.2, 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).
`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
`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)

[Package maftools version 1.6.15 Index]