volcano_plot.DMRcate: Plot for a DMRcate output

In nickfishbane/DMRtools: Tools for 450K differential methylation analysis

Description

Volcano-style plot of effect-size vs. significance with size of DMR represented

Usage

volcano_plot.DMRcate(res.obj, pval.fld = c("mean", "min"), pthresh = 0.01,
  contrast.thresh = 0.25, min.p = 1e-100, xlabel = "max beta difference",
  ylabel = "-log10 p-value", title = "", label.thresh = 0.001,
  colors = c(neut = "darkgrey", low = "red", high = "blue"))

Arguments

res.obj	A dmrcate.output object
pval.fld	Which p-value from DMRcate analysis to plot, either the mean p-value in the DMR ('mean') or the minimum p-value ('min').
pthresh	Numeric value signifying the maximum p-value at which DMRs should be colored
contrast.thresh	Numeric value signifying the threshold for maximum absolute effect size at which DMRs should be colored.
min.p	Numeric minimum value for plotted p-values. Gives an upper limit to the y-axis
xlabel, ylabel, title	Text labels for axis and main titles in plot
label.thresh	Value for maximum p-value threshold with which to label points with gene names
colors	for neutral, hypomethylated, and hypermethylated regions, respectively

Details

Each DMR in the input object will be colored according to whether they are considered hypermethylated in the reference group, hypomethylated, or neither. This will be determined by user-specified p-value and effect-size thresholds

Value

A ggplot object.

nickfishbane/DMRtools documentation built on May 23, 2019, 4:47 p.m.