EnrichedGeneView: Visualize enriched pathways and genes in those pathways

Description Usage Arguments Value Author(s) Examples

View source: R/EnrichedGeneView.R

Description

Visualize enriched pathways and genes in those pathways

Usage

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EnrichedGeneView(
  enrichment,
  geneList,
  rank_by = "p.adjust",
  top = 5,
  bottom = 0,
  keytype = "Symbol",
  gene_cutoff = c(-log2(1.5), log2(1.5)),
  custom_gene = NULL,
  charLength = 40,
  filename = NULL,
  width = 7,
  height = 5,
  ...
)

Arguments

enrichment

A data frame of enrichment result or an enrichResult object.

geneList

A numeric geneList used in enrichment anlaysis.

rank_by

"p.adjust" or "NES", specifying the indices for ranking pathways.

top

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

bottom

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

keytype

"Entrez" or "Symbol".

gene_cutoff

A two-length numeric vector, specifying cutoff for genes to show.

custom_gene

A character vector (gene names), customizing genes 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

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data(geneList, package = "DOSE")
## Not run: 
  enrichRes <- enrich.GSE(geneList, keytype = "Entrez")
  EnrichedGeneView(enrichment=slot(enrichRes, "result"), geneList, keytype = "Entrez")

## End(Not run)

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.