volcanoplot_topTable_PandQ: A wrapper function to plot 2 volcano plots side by side, for...

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

A wrapper function to plot 2 volcano plots side by side, for the logFC vs P and q values.

Usage

  volcanoplot_topTable_PandQ(tt, pThresh = 0.001,
    qThresh = 0.05, lfc = log2(1.5), cex.points = 0.5,
    ablines = "", ...)

Arguments

tt	a data.frame object from calling topTable with all genes.
pThresh	For colouring significant points in the p-value panel., default=0.001
qThresh	For colouring significant points in the FDR panel., default=0.05
lfc	the absolute log fold change threshold. eg 0.585 for 1.5 FC, or 1.0 for a 2-fold change
cex.points	see par
ablines	whether to add vertical dashed lines at yThresh and xThresh. “”, “x”, “y”, or “xy” for none, x (ie vertical lines at +/- xThresh only), y (ie horizontal line at yThresh only), x and y
...	further arguments passed to volcanoplot_topTable

Author(s)

Mark Cowley, 2008-08-01

See Also

volcanoplot_topTable

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.