ddgraph (version 1.16.0)

plotPCalg: Plot the network inferred by the PC algorithm

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

# 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)