enrichmentPlot {transcriptogramer} | R Documentation |
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.
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)
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 |
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. |
This method returns an ggplot2 object.
Diego Morais
differentiallyExpressed, transcriptogramPreprocess, GSE9988, GPL570, Hs900, HsBPTerms, association, transcriptogramStep1, transcriptogramStep2, clusterEnrichment
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)