enrichmentPlot-method: Projects Gene Ontology terms on the ordering

In arthurvinx/transcriptogramer: Transcriptional analysis based on transcriptograms

Projects Gene Ontology terms on the ordering

Description

Plots the ratio (number of genes related to a term inside the window/total number of genes in the window) from a set of Gene Ontology 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)

arthurvinx/transcriptogramer documentation built on March 21, 2023, 9:15 a.m.