plotSoftPower: Plot Soft Power Fit and Connectivity

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

Plot Soft Power Fit and Connectivity

Description

plotSoftPower() visualizes scale-free topology fit and mean connectivity for multiple soft power thresholds as a scatterplot, and then saves it as a .pdf.

Usage

plotSoftPower(
  sft,
  pointCol = "#132B43",
  lineCol = "red",
  nBreaks = 4,
  save = TRUE,
  file = "Soft_Power_Plots.pdf",
  width = 8.5,
  height = 4.25,
  verbose = TRUE
)

Arguments

sft	A list produced by getSoftPower() with two elements: powerEstimate and fitIndices.
pointCol	A character(1) specifying the color of the points.
lineCol	A character(1) giving the color of line and label for the estimated soft power threshold for scale-free topology.
nBreaks	A numeric(1) specifying the number of breaks used 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

plotSoftPower() is designed to be used in combination with getSoftPower(). A ggplot object is produced and can be edited outside of this function if desired.

Value

A ggplot object.

See Also

• getRegionMeth(), getPCs(), and adjustRegionMeth() to extract methylation data and then adjust it for the top principal components.

• getSoftPower() to calculate the best soft-thresholding power and fit indices for scale-free topology.

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

Examples

## Not run: 

# Get Methylation Data
meth <- getRegionMeth(regions, bs = bs, file = "Region_Methylation.rds")

# Adjust Methylation Data for PCs
mod <- model.matrix(~1, data = pData(bs))
PCs <- getPCs(meth, mod = mod, file = "Top_Principal_Components.rds")
methAdj <- adjustRegionMeth(meth, PCs = PCs,
                            file = "Adjusted_Region_Methylation.rds")

# Select Soft Power Threshold
sft <- getSoftPower(methAdj, corType = "pearson", file = "Soft_Power.rds")
plotSoftPower(sft, file = "Soft_Power_Plots.pdf")

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

## End(Not run)

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