plotTRM: Plot an annotated TRM.

In rTRM: Identification of transcriptional regulatory modules from PPI networks

Description

This function plots the output findTRM() after it has been annotated with cluster information with annotateTRM() function. Cluster membership is plotted using a pie plot.

Usage

plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)

Arguments

g	a network object with cluster information (attribute piecolor).
layout	graph layout, either a function or the output of a layout function.
mar	plot margin.
vertex.col	node color.
vertex.cex	node size.
vertex.lwd	node border line width.
edge.col	edge color.
edge.lwd	edge line width.
edge.lty	edge line type.
label	logical; whether to plot labels.
label.cex	label expansion.
label.col	label color.
label.pos	label position.
label.offset	label offset.
adjust.label.col	whether to automatically adjust label color depending on the luminance of the node's color.
normalize.layout	whether to apply layout.norm (with limits xmin=-1, xmax=1, ymin=-1, ymax=1) to the layout.

Author(s)

Diego Diez

rTRM documentation built on Nov. 8, 2020, 5:52 p.m.