drawVolcanoPlot {maDB}R Documentation

Draw a volcano plot

Description

drawVolcanoPlot plots a volcano plot scattering the M values (log2 ratio) on the x axis against the p value (-log10 the p value).

Usage

drawVolcanoPlot(M,p,m=1,p.cut=0.05,p.transform=log10,ylab=NULL,colramp=NULL,na.rm=TRUE,...)

Arguments

M The M values.
p The test statistics (usually p values).
m Where vertical lines should be drawn. By default two horizontal lines (at M=1 and M=-1) are added to the plot. Submit m=NA if none should be drawn.
p.cut For what p value a horizontal line should be added to the plot (by default for a p value of p=0.05). Specify p.cut=NA if no line should be drawn.
p.transform The function that should be applied to the p values. By default -log10. Note a - is added to each function submitted here.
ylab The label for the y axis. By default -log10(p)
colramp A color ramp (set of colors) that should be used to code the local point desity. This attribute requires the package geneplotter as the densCols function is used to calculate the local point density.
na.rm If NA values should be removed.
... Additional parameters for the plot function.

Details

This function plots M values against test statistics. A horizontal line for a specific p value (by default 0.05) is added as well as vertical lines for a specific M value (by default 1 and -1). The data points can be colored according to the local point density by specifying a specific color ramp (e.g. colramp=topo.colors).

Author(s)

Johannes Rainer


[Package maDB version 1.14.1 Index]