iplotPC: Plotting a pcAlgo object using the package igraph

In pcalg: Methods for Graphical Models and Causal Inference

Plotting a pcAlgo object using the package igraph

Description

Notably, when the Rgraphviz package is not easily available, iplotPC() is an alternative for plotting a "pcAlgo" object, making use of package igraph.

It extracts the adjacency matrix and converts it into an object from package igraph which is then plotted.

Usage

iplotPC(pc.fit, labels = NULL)

Arguments

pc.fit	an R object of class pcAlgo, as returned from skeleton() or pc().
labels	optional labels for nodes; by default, the labels from the pc.fit object are used.

Value

Nothing. As side effect, the plot of pcAlgo object pc.fit.

Note

Note that this function does not work on fciAlgo objects, as those need different edge marks.

Author(s)

Markus Kalisch [e-mail]

See Also

showEdgeList for printing the edge list of a pcAlgo object; showAmat for printing the adjacency matrix of a pcAlgo object.

Examples

## Load predefined data
data(gmG)
n <- nrow    (gmG8$x)
V <- colnames(gmG8$x)

## define sufficient statistics
suffStat <- list(C = cor(gmG8$x), n = n)
## estimate CPDAG
pc.fit <- pc(suffStat, indepTest = gaussCItest,
             alpha = 0.01, labels = V, verbose = TRUE)

## Edge list
showEdgeList(pc.fit)

## Adjacency matrix
showAmat(pc.fit)

## Plot using package igraph; show estimated CPDAG:
iplotPC(pc.fit)

pcalg documentation built on Sept. 26, 2023, 9:06 a.m.