prune.cna {bio3d}

Prune A cna Network Object

Description

Remove nodes and their associated edges from a cna network graph.

Usage

prune.cna(x, edges.min = 1, size.min = 1)

Arguments

x

A protein network graph object as obtained from the ‘cna’ function.

edges.min

A single element numeric vector specifying the minimum number of edges that retained nodes should have. Nodes with less than ‘edges.min’ will be pruned.

size.min

A single element numeric vector specifying the minimum node size that retained nodes should have. Nodes with less composite residues than ‘size.min’ will be pruned.

Details

This function is useful for cleaning up cna network plots by removing, for example, small isolated nodes. The output is a new cna object minus the pruned nodes and their associated edges. Node naming is preserved.

Value

A cna class object, see function cna for details.

Note

Some improvements to this function are required, including a better effort to preserve the original community structure rather than calculating a new one. Also may consider removing nodes form the raw.network object that is returned also.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

cna, summary.cna, vmd.cna, plot.cna

Examples

if (!requireNamespace("igraph", quietly = TRUE)) {
   message('Need igraph installed to run this example')
} else {

# Load the correlation network
attach(hivp)

# Read the starting PDB file to determine atom correspondence
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)

# Plot coarse grain network based on dynamically coupled communities
par(mfcol=c(1,2), mar=c(0,0,0,0))
plot.cna(net)

# Prune network
dnet <- prune.cna(net, edges.min = 1)
plot(dnet)

detach(hivp)

}