EnrichedGeneView {MAGeCKFlute} | R Documentation

## 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 = 5, custom_pid = NULL, 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.
`custom_pid` | A character vector (pathway IDs), customizing pathways 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")
    enrichRes <- enrich.GSE(geneList)
    EnrichedGeneView(enrichment=slot(enrichRes, "result"), geneList, keytype = "Entrez")

[Package MAGeCKFlute version 1.4.3 Index]