plotGSEA: plot multiple significant pathways with enhanced...

In guokai8/richR: Function Enrichment analysis and Network construction

plot multiple significant pathways with enhanced customization

Description

plot multiple significant pathways with enhanced customization

Usage

plotGSEA(
  object,
  gseaRes,
  mycol = NULL,
  pathways = NULL,
  pathway_pattern = NULL,
  category = NULL,
  min_genes = NULL,
  max_genes = NULL,
  top = 10,
  pvalue = 0.05,
  padj = NULL,
  gseaParam = 1,
  ticksSize = 0.2,
  plot_title = "GSEA Enrichment Plot",
  show_pathway_names = FALSE,
  pathway_name_size = 10,
  line_alpha = 0.8,
  point_alpha = 0.6,
  return_data = FALSE,
  interactive = FALSE
)

Arguments

object	Annot object
gseaRes	GSEAResult object
mycol	a vector indicate the colors used for the figure
pathways	specific pathway names to display (if NULL, use top/pvalue/padj filtering)
pathway_pattern	regex pattern for pathway matching
category	pathway category filter
min_genes	minimum gene set size filter
max_genes	maximum gene set size filter
top	number of terms you want to display (used when pathways is NULL)
pvalue	cutoff value of pvalue (if padj set as NULL, used when pathways is NULL)
padj	cutoff value of p adjust value (used when pathways is NULL)
gseaParam	GSEA parameter for enrichment score calculation
ticksSize	size of the tick marks
plot_title	title for the plot
show_pathway_names	whether to show pathway names on plot
pathway_name_size	size of pathway name text
line_alpha	transparency of lines
point_alpha	transparency of points
return_data	whether to return plot data along with plot
interactive	whether to create interactive plot using plotly

Author(s)

Kai Guo

Examples

## Not run: 
set.seed(123)
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
name=sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene)<-name
res<-richGSEA(gene,object = hsako)
# Plot top 10 significant pathways
plotGSEA(object = hsako, gseaRes = res)
# Plot specific pathways
plotGSEA(object = hsako, gseaRes = res,
         pathways = c("MAPK signaling pathway", "PI3K-Akt signaling pathway"))
# Plot pathways matching pattern
plotGSEA(object = hsako, gseaRes = res, pathway_pattern = "signaling")
# Interactive plot
plotGSEA(object = hsako, gseaRes = res, interactive = TRUE)

## End(Not run)

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