gdcEnrichPlot: Plots for enrichment analysis

In Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

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')

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.