EnrichedGeneView {MAGeCKFlute}R Documentation

Visualize selected genes in enriched genesets

Description

Visualize selected genes in enriched genesets

Usage

EnrichedGeneView(enrichment, geneList, keytype = "Symbol",
  gene_cutoff = c(-log2(1.5), log2(1.5)), top = 5, bottom = 5,
  charLength = 40, filename = NULL, width = 7, height = 5, ...)

Arguments

enrichment

A data frame of enrichment result.

geneList

The geneList used in enrichment analysis.

keytype

"Entrez" or "Symbol".

gene_cutoff

A tow-length numeric vector, specifying cutoff for negative and positive selections.

top

An integer, specifying the number of top enriched terms to show.

bottom

An integer, specifying the number of bottom enriched terms to show.

charLength

Integer, specifying max length of enriched term name to show as coordinate lab.

filename

Figure file name to create on disk. Default filename="NULL", which means no output.

width

As in ggsave.

height

As in ggsave.

...

Other available parameters in ggsave.

Value

An object created by ggplot, which can be assigned and further customized.

Author(s)

Wubing Zhang

Examples

data(geneList, package = "DOSE")
enrichRes <- enrich.GSE(geneList)
EnrichedGeneView(enrichment=as.data.frame(enrichRes), geneList, keytype = "Entrez")

[Package MAGeCKFlute version 1.2.3 Index]