EnrichedGeneView: Visualize enriched pathways and genes in those pathways

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Visualize enriched pathways and genes in those pathways

Description

Visualize enriched pathways and genes in those pathways

Usage

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

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

## End(Not run)

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.