pcalg: iplotPC – R documentation

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iplotPC

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 kalisch@stat.math.ethz.ch

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

Methods for Graphical Models and Causal Inference

v2.7-2

GPL (>= 2)

Authors

Markus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb], Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb], Marco Eigenmann [ctb], Leonard Henckel [ctb], Joris Mooij [ctb]

Initial release

2021-4-20