EnrichedView {MAGeCKFlute} | R Documentation

## View enriched terms

### Description

Grid plot for enriched terms

### Usage

    EnrichedView(
      enrichment,
      rank_by = "pvalue",
      mode = 1,
      subset = NULL,
      top = 0,
      bottom = 0,
      x = "LogFDR",
      charLength = 40,
      filename = NULL,
      width = 7,
      height = 4,
      ...
    )

### Arguments

`enrichment` | A data frame of enrichment result, with columns of ID, Description, p.adjust and NES.
`rank_by` | "pvalue" or "NES", specifying the indices for ranking pathways.
`mode` | 1 or 2.
`subset` | A vector of pathway ids.
`top` | An integer, specifying the number of positively enriched terms to show.
`bottom` | An integer, specifying the number of negatively enriched terms to show.
`x` | Character, "NES", "LogP", or "LogFDR", indicating the variable on the x-axis.
`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".
`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

### See Also

`EnrichedView`

### Examples

    data(geneList, package = "DOSE")
    ## Not run:
        enrichRes = enrich.GSE(geneList, organism="hsa")
        EnrichedView(slot(enrichRes, "result"))

    ## End(Not run)

[Package MAGeCKFlute version 1.7.2 Index]