plotEnrichment: Plot Functional Enrichment Results

In cemordaunt/comethyl: An R Package for Weighted Region Comethylation Network Analysis

Plot Functional Enrichment Results

Description

plotEnrichment() takes a data.frame of enrichment results from enrichModule(), plots the log p-values in a bar plot, and saves it as a .pdf.

Usage

plotEnrichment(
  enrichment,
  nTerms = 15,
  fill = "#132B43",
  xlim = NULL,
  nBreaks = 4,
  axis.title.x.size = 20,
  axis.text.x.size = 16,
  axis.text.y.size = 16,
  save = TRUE,
  file = "Module_Enrichment_Plot.pdf",
  width = 8,
  height = 6,
  verbose = TRUE
)

Arguments

enrichment	A data.frame of functional enrichment results, typically obtained from enrichModule().
nTerms	A numeric(1) specifying the number of terms to include in the plot.
fill	A character(1) giving the color of the bars.
xlim	A numeric(2) specifying the limits of the x-axis.
nBreaks	A numeric(1) indicating the number of breaks to use in the x-axis.
axis.title.x.size	A numeric(1) with the size of the x-axis title.
axis.text.x.size	A numeric(1) giving the size of the x-axis text.
axis.text.y.size	A numeric(1) giving the size of the y-axis text.
save	A logical(1) indicating whether to save the plot.
file	A character(1) giving the file name (.pdf) for the saved plot.
width	A numeric(1) specifying the width in inches of the saved plot.
height	A numeric(1) specifying the height in inches of the saved plot.
verbose	A logical(1) indicating whether messages should be printed.

Details

plotEnrichment() is designed to be used in combination with enrichModule(). The top 15 gene sets are plotted by default, but this can be expanded if needed. A ggplot object is produced and can be edited outside of this function if desired.

Value

A ggplot object.

See Also

• getModules() to build a comethylation network and identify modules of comethylated regions.

• annotateModule() and getGeneList() to annotate a set of regions with genes and regulatory context and then extract the gene symbols or IDs.

• listOntologies() and enrichModule(), to investigate functional enrichment of module regions with GREAT.

Examples

## Not run: 

# Get Comethylation Modules
modules <- getModules(methAdj, power = sft$powerEstimate, regions = regions,
                      corType = "pearson", file = "Modules.rds")

# Annotate Modules
regionsAnno <- annotateModule(regions, module = "bisque4",
                              genome = "hg38",
                              file = "Annotated_bisque4_Module_Regions.txt")
geneList_bisque4 <- getGeneList(regionsAnno, module = "bisque4")

# Analyze Functional Enrichment
ontologies <- listOntologies("hg38", version = "4.0.4")
enrich_bisque4 <- enrichModule(regions, module = "bisque4",
                               genome = "hg38",
                               file = "bisque4_Module_Enrichment.txt")
plotEnrichment(enrich_bisque4,
               file = "bisque4_Module_Enrichment_Plot.pdf")

## End(Not run)

cemordaunt/comethyl documentation built on Oct. 20, 2023, 5:47 p.m.