plotMethTrait: Plot Module Methylation Values By a Sample Trait

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

Plot Module Methylation Values By a Sample Trait

Description

plotMethTrait() extracts the methylation values for regions in a given module, plots it against a sample trait in a heatmap, and then saves it as a .pdf. trait must be in the same order as the columns in meth.

Usage

plotMethTrait(
  module,
  regions,
  meth,
  trait,
  discrete = NULL,
  traitCode = NULL,
  traitColors = NULL,
  heatmapColors = blueWhiteRed(100, gamma = 0.3),
  limit = NULL,
  expandY = 0.05,
  axis.text.size = 11,
  heatmap.legend.position = c(1.1, 0.743),
  trait.legend.position = c(1.017, 4.39),
  heatmap.legend.title = "Relative\nMethylation (%)",
  trait.legend.title = "Trait",
  legend.text.size = 11,
  legend.title.size = 14,
  heatmapMargins = c(1, 8, 0, 1),
  traitMargins = c(0, 6, 1, 5.15),
  save = TRUE,
  file = "Module_Methylation_Trait_Heatmap.pdf",
  width = 11,
  height = 4,
  verbose = TRUE
)

Arguments

module	A character(1) giving the name of the module to plot.
regions	A data.frame of regions with module assignments, typically obtained from getModules().
meth	A numeric matrix, where each row is a region and each column is a sample. This is typically obtained from getRegionMeth().
trait	A numeric of sample trait values.
discrete	A logical(1) identifying trait as a discrete variable or not. If null, plotMethTrait() will guess if the trait is discrete (<= 5 unique values).
traitCode	A named numeric vector matching each trait level to a numeric value. Example: c("Control" = 0, "Treatment" = 1).
traitColors	A named character vector matching each trait level to a color. Example: c("Control" = "blue", "Treatment" = "red").
heatmapColors	A character giving a vector of colors to use for the gradient on the heatmap. The default uses WGCNA::blueWhiteRed() to generate these colors.
limit	A numeric(1) giving the maximum value (symmetric) for the heatmap color scale.
expandY	A numeric specifying the multiplicative range expansion factors. Can be given as the symmetric lower and upper limit expansions or separately as a vector of length 2.
axis.text.size	A numeric(1) giving the size of the text on the y-axis.
heatmap.legend.position	A numeric(2) with the position of the heatmap legend, as x-axis, y-axis. May also be a character(1) indicating "none", "left", "right", "bottom", or "top".
trait.legend.position	A numeric(2) with the position of the color bar legend, as x-axis, y-axis. May also be a character(1) indicating "none", "left", "right", "bottom", or "top".
heatmap.legend.title	A character(1) giving the title for the heatmap legend.
trait.legend.title	A character(1) giving the title for the color bar legend.
legend.text.size	A numeric(1) indicating the size the text in both legends.
legend.title.size	A numeric(1) specifying the size of the text for both legend titles.
heatmapMargins	A numeric(4) giving the width of the margins for the heatmap as top, right, bottom, and left.
traitMargins	A numeric(4) giving the width of the margins for the color bar as top, right, bottom, and left.
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

NA values in the trait are removed if present, along with corresponding ME values. If discrete is not provided plotMethTrait() will guess if the trait is discrete (<= 5 unique values) and plot the trait color as a discrete scale rather than a continuous one. Samples are ordered by trait value in ascending order. Methylation values are plotted relative to the mean methylation in that region.

Value

A ggplot object.

See Also

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

• getMEtraitCor() and plotMEtraitCor() to calculate and visualize all ME-trait correlations.

• plotMEtraitDot() and plotMEtraitScatter() for other methods to visualize a single ME-trait correlation.

Examples

## Not run: 

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

# Test Correlations between Module Eigennodes and Sample Traits
MEs <- modules$MEs
MEtraitCor <- getMEtraitCor(MEs, colData = colData, corType = "bicor",
                            file = "ME_Trait_Correlation_Stats.txt")
plotMEtraitCor(MEtraitCor, moduleOrder = moduleDendro$order,
               traitOrder = traitDendro$order,
               file = "ME_Trait_Correlation_Heatmap.pdf")

# Explore Individual ME-Trait Correlations
plotMEtraitDot(MEs$bisque4, trait = colData$Diagnosis_ASD,
               traitCode = c("TD" = 0, "ASD" = 1),
               colors = c("TD" = "#3366CC", "ASD" = "#FF3366"),
               ylim = c(-0.2,0.2), xlab = "Diagnosis",
               ylab = "Bisque 4 Module Eigennode",
               file = "bisque4_ME_Diagnosis_Dotplot.pdf")
plotMEtraitScatter(MEs$paleturquoise, trait = colData$Gran,
                   ylim = c(-0.15,0.15), xlab = "Granulocytes",
                   ylab = "Pale Turquoise Module Eigennode",
                   file = "paleturquoise_ME_Granulocytes_Scatterplot.pdf")
regions <- modules$regions
plotMethTrait("bisque4", regions = regions, meth = meth,
              trait = colData$Diagnosis_ASD,
              traitCode = c("TD" = 0, "ASD" = 1),
              traitColors = c("TD" = "#3366CC", "ASD" = "#FF3366"),
              trait.legend.title = "Diagnosis",
              file = "bisque4_Module_Methylation_Diagnosis_Heatmap.pdf")

## End(Not run)

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