ggdot: dotplot for Enrichment results

In hurlab/RichR: Function Enrichment analysis and Network construction

dotplot for Enrichment results

Description

dotplot for Enrichment results

dotplot for Enrichment results

Usage

## S4 method for signature 'richResult'
ggdot(
  object,
  top = 50,
  pvalue = 0.05,
  order = FALSE,
  low = "lightpink",
  high = "red",
  alpha = 0.7,
  font.x = "bold",
  font.y = "bold",
  fontsize.x = 10,
  fontsize.y = 10,
  short = FALSE,
  padj = NULL,
  usePadj = TRUE,
  orderp = FALSE,
  filename = NULL,
  width = 10,
  height = 8
)

## S4 method for signature 'data.frame'
ggdot(
  object,
  top = 50,
  pvalue = 0.05,
  order = FALSE,
  low = "lightpink",
  high = "red",
  alpha = 0.7,
  font.x = "bold",
  font.y = "bold",
  fontsize.x = 10,
  fontsize.y = 10,
  short = FALSE,
  padj = NULL,
  usePadj = TRUE,
  orderp = FALSE,
  filename = NULL,
  width = 10,
  height = 8
)

Arguments

object	richResult object
top	number of terms you want to display,
pvalue	cutoff value of pvalue (if padj set as NULL)
order	order by Term or richFactor
low	low color
high	high color
alpha	transparency alpha
font.x	font of x 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)
orderp	order by p value(adjusted p value)
filename	figure output name
width	figure width
height	figure height
font	y font of y axis
font.size	font size for xlim or ylim

Author(s)

Kai Guo

Examples

## Not run: 
  hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
  gene=sample(unique(hsako$GeneID),1000)
  res<-richKEGG(gene,kodata = hsako)
  ggdot(res)

## End(Not run)
## Not run: 
  hsago<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
  gene=sample(unique(hsago$GeneID),1000)
  res<-richKEGG(gene,kodata = hsako)
  ggdot(result(res))

## End(Not run)

hurlab/RichR documentation built on Feb. 5, 2024, 8:07 p.m.