drawVolcanoPlot {maDB} | R Documentation |
drawVolcanoPlot
plots a volcano plot scattering the M values (log2 ratio) on the x axis against the p value (-log10 the p value).
drawVolcanoPlot(M,p,m=1,p.cut=0.05,p.transform=log10,ylab=NULL,colramp=NULL,na.rm=TRUE,...)
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. |
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
).
Johannes Rainer