DGOnetplot: Draw a gene association network of DO and GO enrichment...

In JoelleJee/DGOplot: DO and GO Enrichment Analyses Plotting

Description

A function that draws a gene association network with DO and GO terms from enrichment analyses.

Usage

DGOnetplot(
  DGOResult,
  showCategory = 6,
  pAdjustCutoff = 0.05,
  cluster.strength = 10,
  GOcol = c("blue", "lightblue"),
  DOcol = c("red", "mistyrose"),
  termCol = "PuOr",
  geneCol = "honeydew3"
)

Arguments

DGOResult	DO and GO enrichment analysis result returned from enrichDGO().
showCategory	number of ontology groups to show from DO and GO each.
pAdjustCutoff	p-value cutoff.
cluster.strength	clustering strength of each ontology group on the network graph
GOcol	vector of colors for gradient GO edges
DOcol	vector of colors for gradient DO edges
termCol	name of ColorBrewer color palettes for ontology term nodes
geneCol	color of gene nodes

Value

Returns a gene association network of DO and GO analyses.

• edges colored in gradient according to p.adjust value

• edges to DO and GO terms colored differently

• ontology term nodes size proportional to number of genes associated with it

Examples

## Not run: 
# load data from DOSE
library(DOSE)
data(geneList)
gene <- names(geneList)[abs(geneList) > 2]
result <- enrichDGO(gene, universe=names(geneList))

# tamper the data little bit to see 
# the full functionalities of DGOplot
result$DO@result$p.adjust <-  result$DO@result$p.adjust / 10

DGOnetplot(result)
DGOnetplot(result,
           showCategory = 4,
           cluster.strength = 5)

## End(Not run)

JoelleJee/DGOplot documentation built on July 15, 2020, 8:32 a.m.