bio3d (version 2.3-3)

print.cna: Summarize and Print Features of a cna Network Graph

Description

These functions attempt to summarize and print a cna network graph to the terminal in a human readable form.

Usage

# S3 method for cna
print(x, ...)
  # S3 method for cna
summary(object, verbose=TRUE, ...)

Arguments

x

A cna network and community object as obtained from the function ‘cna’.

object

A cna network and community object as obtained from the function ‘cna’.

verbose

Logical, if TRUE a community summary table is prited to screen.

…

Extra arguments passed to the ‘write.table’ function.

Value

The function summary.cna returns a list with the following components:

id

A community number/identifier vector with an element for each community.

size

A numeric community size vector, with elements giving the number of nodes within each community.

members

A lst detailing the nodes within each community.

Details

Simple summary and print methods for protein dynamic networks.

References

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

See Also

cna, print.igraph, str.igraph, igraph.plotting

Examples

# NOT RUN {
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)

## Examine network composition
print(net)
x<- summary(net)
x$members[[2]]

detach(hivp)

}
# }