plotPCalg: Plot the network inferred by the PC algorithm

In ddgraph: Distinguish direct and indirect interactions with Graphical Modelling

Description

Infer a network using PC algorithm and plot it.

Usage

plotPCalg(d, name, alpha=0.05, verbose=FALSE, directed=TRUE, make.plot=FALSE,
    scale=1.5, indepTest=mcX2Test, class.label="target",
    use.colors=TRUE)

Arguments

d	DDDataSet object
name	the name to show (defaults to dataset name)
alpha	the alpha value cut-off for the conditional independence tests
verbose	if to show progress
directed	if TRUE applies PC algorithm, if FALSE applies PC-skeleton
make.plot	if to output the plot into the active device
scale	the scaling parameter for color-coding
indepTest	the independence test wrapper function (as needed by package pcalg)
class.label	the label to show for class variable
use.colors	if to color code the results

Examples

data(mesoBin)
# use PC algorithm to construct a causal network and colour it according to enrichment/depletion
plotPCalg(mesoBin$Meso, alpha=0.05, directed=TRUE, make.plot=TRUE)

ddgraph documentation built on Nov. 17, 2017, 10:50 a.m.