comparedot: draw dotplot for multiple enrichment results

In guokai8/richR: Function Enrichment analysis and Network construction

draw dotplot for multiple enrichment results

Description

draw dotplot for multiple enrichment results

Usage

comparedot(
  x,
  pvalue = 0.05,
  low = "lightpink",
  high = "red",
  level = "Level3",
  pathway = NULL,
  alpha = 0.7,
  font.x = "bold",
  font.y = "bold",
  fontsize.x = 10,
  fontsize.y = 10,
  short = FALSE,
  padj = NULL,
  usePadj = TRUE,
  filename = NULL,
  width = 10,
  height = 8,
  include.all = FALSE
)

Arguments

x	dataframe of enrichment result
pvalue	cutoff value of pvalue (if padj set as NULL)
low	low color
high	high color
level	the level for KEGG pathway
pathway	the KEGG pathway name for the level
alpha	transparency alpha
font.x	font of x axis
font.y	font of y axis
fontsize.x	fontsize of x axis
fontsize.y	fontsize of y axis
short	automatic short name or not
padj	cutoff value of p adjust value
usePadj	use p adjust value as color or not (should use with padj)
filename	figure output name
width	figure width
height	figure height
include.all	include all richResults even empty

Author(s)

Kai Guo

Examples

## Not run: 
hsako <- buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
hsago <- buildAnnot(species="human",keytype="SYMBOL",anntype = "GO")
gene1 <- sample(unique(hsako$GeneID),1000)
gene2 <- sample(unique(hsako$GeneID),1000)
resko1 <-richKEGG(gene1,kodata = hsako)
resko2 <-richKEGG(gene2,kodata = hsako)
res<-compareResult(list(S1=resko1,S2=resko2))
comparedot(res,pvalue=0.05)

## End(Not run)

guokai8/richR documentation built on June 10, 2025, 4:51 a.m.