gdcEnrichPlot {GDCRNATools} | R Documentation

## Plots for enrichment analysis

### Description

Bar plot and bubble plot for GO, KEGG, and DO functional enrichment analysis

### Usage

    gdcEnrichPlot(enrichment, type = "bar", category = "KEGG",
      num.terms = 10, bar.color = "black")

### Arguments

`enrichment` | a dataframe generated from `gdcEnrichAnalysis`
`type` | type of the plot, should be one of `'bar'` and `'bubble'`
`category` | which category should be plotted. Possible values are `'KEGG'`, `'GO'`, `'GO_BP'`, `'GO_CC'`, `'GO_MF'`, and `'DO'`. Default is `'KEGG'`
`num.terms` | number of terms to be plotted. Default is `10`
`bar.color` | color of the bar plot. Default is `'black'`

### Value

A bar plot or bubble plot of functional enrichment analysis

### Author(s)

Ruidong Li and Han Qu

### Examples

    ####### Enrichment plots #######
    enrichOutput<-data.frame(Terms=c('hsa05414~Dilated cardiomyopathy (DCM)',
                                    'hsa04510~Focal adhesion',
                                    'hsa05205~Proteoglycans in cancer'),
                                Category=rep('KEGG',3),
                                FDR=c(0.001,0.002,0.003))
    gdcEnrichPlot(enrichment=enrichOutput, type='bar', category='KEGG')

[Package GDCRNATools version 1.13.1 Index]