assocPvalBySetPlot {cpvSNP} | R Documentation |
Plots association test p-values, highlighting p-values within gene sets.
assocPvalBySetPlot(pvals, set, title = "", geneSetColor = "red", xlab = expression(-log[10]~p-value), ylab = "Density", xlim = NULL, ylim = NULL, ...)
pvals |
A numerical vector of p-values with names corresponding to elements listed in the geneIds slot in the set object. |
set |
An object of class |
title |
A character string containing the title of the plot. Default is "", a blank title. |
geneSetColor |
A character vector holding the color the
highlighted SNPs in the set object should be. Default is
|
xlab |
A character vector with the label for the x-axis on
the plot. Default is |
ylab |
A character vector holding the label for the y-axis
on the plot. Default is |
xlim |
A vector of two numeric values with the limits of plotting on the x-axis. By default, the range of the x-axis values will be determined from the data. |
ylim |
A vector with two numeric values used as limits for plotting on the y-axis. By default, the range of the y-axis values will be determined from the data. |
... |
Further arguments to be passed to the plotting methods, such as graphical parameters. |
Creates a density plot of all -log10(p-value), and overlaying a density plot of -log10(p-value) for SNPs within a gene set of interest.
Creates a plot.
Jason Hackney, Jessica Larson, Caitlin McHugh mchughc@uw.edu