plotModulePreservation: Visualize Module Preservation

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

Visualize Module Preservation

Description

plotModulePreservation() plots Z-scores for various module preservation statistics by module size as a scatterplot, and then saves it as a .pdf.

Usage

plotModulePreservation(
  preservation,
  line.size = 0.9,
  point.size = 1.2,
  nBreaks = 3,
  strip.text.size = 8.5,
  axis.text.size = 10,
  axis.title.size = 12,
  save = TRUE,
  file = "Module_Preservation_Plots.pdf",
  width = 9,
  height = 9,
  verbose = TRUE
)

Arguments

preservation	A data.frame of module preservation statistics for each module, generated by getModulePreservation().
line.size	A numeric(1) giving the size of the horizontal lines.
point.size	A numeric(1) indicating the size of the points.
nBreaks	A numeric(1) specifying the number of breaks used for both axes.
strip.text.size	A numeric(1) indicating the size of the title text for each plot.
axis.text.size	A numeric(1) specifying the size of the text for both axes.
axis.title.size	A numeric(1) indicating the size of the title text for both axes.
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

plotModulePreservation() is designed to be used in combination with getModulePreservation(). A blue line is plotted at Z = 2 to indicate weak to moderate evidence for preservation, while a green line is plotted at Z = 10 to indicate strong evidence. A ggplot object is produced and can be edited outside of this function if desired. More information is given in the documentation for WGCNA::modulePreservation().

Value

A ggplot object.

See Also

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

• getModulePreservation() to calculate module preservation statistics.

Examples

## Not run: 
# Calculate Module Preservation
regions_disc <- modules_disc$regions
regions_rep <- modules_rep$regions
preservation <- getModulePreservation(methAdj_disc,
                                      regions_disc = regions_disc,
                                      meth_rep = methAdj_rep,
                                      regions_rep = regions_rep,
                                      corType = "pearson",
                                      file = "Module_Preservation_Stats.txt")

# Visualize Module Preservation
plotModulePreservation(preservation, file = "Module_Preservation_Plots.pdf")

## End(Not run)

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