plotHeatmap: Plot a Heatmap with Dendrograms

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

Plot a Heatmap with Dendrograms

Description

plotHeatmap() takes a numeric matrix and two dendrograms, plots them, and then saves it all as a .pdf. The row names and column names of x must include the same set of values as the labels of rowDendro and colDendro, respectively.

Usage

plotHeatmap(
  x,
  rowDendro,
  colDendro,
  colors = blueWhiteRed(100, gamma = 0.3),
  limit = max(abs(x)),
  axis.text.size = 8,
  legend.title = "Bicor",
  legend.title.size = 16,
  legend.text.size = 12,
  legend.position = c(0.3, 0.905),
  rowDendroMargins = c(-1.55, 1, -0.1, -1.1),
  colDendroMargins = c(1, -0.5, -1, 0.8),
  rowColorMargins = c(-1.85, -1.5, 0.55, 1.7),
  colColorMargins = c(-1.6, -0.85, 1.8, 0.55),
  save = TRUE,
  file = "Heatmap.pdf",
  width = 11,
  height = 9.5,
  verbose = TRUE
)

Arguments

x	A numeric matrix. The row names and column names of x must include the same set of values as the labels of rowDendro and colDendro, respectively.
rowDendro	An stats::hclust object generated by getDendro().
colDendro	An stats::hclust object generated by getDendro().
colors	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.
axis.text.size	A numeric(1) specifying the size of the text for both axes.
legend.title	A character(1) with the title of the legend.
legend.title.size	A numeric(1) giving the size of the text for the legend title.
legend.text.size	A numeric(1) specifying the size of the text for the legend axis.
legend.position	A numeric(2) with the position of the legend, as x-axis, y-axis. May also be a character(1) indicating "none", "left", "right", "bottom", or "top".
rowDendroMargins	A numeric(4) giving the width of the margins for the row (vertical) dendrogram as top, right, bottom, and left.
colDendroMargins	A numeric(4) giving the width of the margins for the column (horizontal) dendrogram as top, right, bottom, and left.
rowColorMargins	A numeric(4) giving the width of the margins for the row (vertical) color bar as top, right, bottom, and left.
colColorMargins	A numeric(4) giving the width of the margins for the column (horizontal) 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

plotHeatmap() is designed to be used in combination with getCor() and getDendro(). The function will check to see if module color names are in the row and column names and then plot a color bar with the module colors. A ggplot object is produced and can be edited outside of this function if desired.

Value

A ggplot object.

See Also

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

• getDendro() and plotDendro() to generate and visualize dendrograms.

• getCor() to calculate correlation coefficients.

Examples

## Not run: 

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

# Examine Correlations between Modules
MEs <- modules$MEs
moduleDendro <- getDendro(MEs, distance = "bicor")
plotDendro(moduleDendro, labelSize = 4, nBreaks = 5,
           file = "Module_ME_Dendrogram.pdf")
moduleCor <- getCor(MEs, corType = "bicor")
plotHeatmap(moduleCor, rowDendro = moduleDendro, colDendro = moduleDendro,
            file = "Module_Correlation_Heatmap.pdf")

# Examine Correlations between Samples
sampleDendro <- getDendro(MEs, transpose = TRUE, distance = "bicor")
plotDendro(sampleDendro, labelSize = 3, nBreaks = 5,
           file = "Sample_ME_Dendrogram.pdf")
sampleCor <- getCor(MEs, transpose = TRUE, corType = "bicor")
plotHeatmap(sampleCor, rowDendro = sampleDendro, colDendro = sampleDendro,
            file = "Sample_Correlation_Heatmap.pdf")

# Visualize Module Eigennode Values
plotHeatmap(MEs, rowDendro = sampleDendro, colDendro = moduleDendro,
            legend.title = "Module\nEigennode",
            legend.position = c(0.37,0.89),
            file = "Sample_ME_Heatmap.pdf")

## End(Not run)

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