plotRegionDendro: Plot Region Dendrograms

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

Plot Region Dendrograms

Description

plotRegionDendro() extracts plotting data from a modules list, plots a region dendrogram with module assignments, and then saves it as a .pdf.

Usage

plotRegionDendro(
  modules,
  save = TRUE,
  file = "Region_Dendrograms.pdf",
  width = 11,
  height = 4.25,
  verbose = TRUE
)

Arguments

modules	A list of module assignments and statistics produced by getModules().
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

plotRegionDendro() is designed to be used in combination with getModules(). This function does not produce a ggplot object, but instead uses WGCNA::plotDendroAndColors() to plot the dendrogram.

Value

None, produces a plot as a side effect.

See Also

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

• getModuleBED() to visualize genomic locations and module assignments.

• getDendro() and plotDendro() to generate and visualize dendrograms for samples, modules, and traits.

Examples

## Not run: 

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

# Visualize Comethylation Modules
plotRegionDendro(modules, file = "Region_Dendrograms.pdf")
BED <- getModuleBED(modules$regions, file = "Modules.bed")

## End(Not run)

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