Plot Functional Enrichment Results

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.

Value

A ggplot object.

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.

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

if (FALSE) {

# 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")
}