enrichmentPlot {transcriptogramer} | R Documentation

## Projects Gene Ontology terms on the ordering

### Description

Plots the rate (number of genes related to a term inside the window/total number of genes in the window) of given terms.

### Usage

    enrichmentPlot(object, nCores = 1L, nTerms = 1L, GOIDs = NULL,
      title = "Enrichment", alpha = 0.15, colors = NULL)

    ## S4 method for signature 'Transcriptogram'
    enrichmentPlot(object, nCores = 1L,
      nTerms = 1L, GOIDs = NULL, title = "Enrichment", alpha = 0.15,
      colors = NULL)

### Arguments

`object` | An object of class Transcriptogram.
`nCores` | An integer number, referring to the number of processing cores to be used; or a logical value, TRUE indicating that all processing cores should be used, and FALSE indicating the use of just one processing core. The default value of this argument is 1.
`nTerms` | An integer number referring to the number of top terms from each cluster. The default value of this argument is 1.
`GOIDs` | A character vector containing the Gene Ontology accessions to be plotted. If NULL, the top `nTerms` of each cluster will be used.
`title` | An overall title for the plot. The default value of this argument is "Enrichment"
`alpha` | The alpha value indicates the color transparency of the clusters regions. This value goes from 0 to 1, where 0 is completely transparent, and 1 is opaque.
`colors` | Color vector used to distinguish the clusters. If NULL, the rainbow palette will be used to generate the colors. The color vector must contain a color for each cluster.

### Value

This method returns an ggplot2 object.

### Author(s)

Diego Morais

### See Also

differentiallyExpressed, transcriptogramPreprocess, GSE9988, GPL570, Hs900, HsBPTerms, association, transcriptogramStep1, transcriptogramStep2, clusterEnrichment

### Examples

    transcriptogram <- transcriptogramPreprocess(association, Hs900, 50)
    ## Not run:
    transcriptogram <- transcriptogramStep1(transcriptogram, GSE9988, GPL570)
    transcriptogram <- transcriptogramStep2(transcriptogram)
    levels <- c(rep(FALSE, 3), rep(TRUE, 3))
    transcriptogram <- differentiallyExpressed(transcriptogram, levels, 0.01)
    transcriptogram <- clusterEnrichment(transcriptogram, species = "Homo sapiens",
    pValue = 0.005)
    enrichmentPlot(transcriptogram)

    ## End(Not run)

[Package transcriptogramer version 1.6.0 Index]