print.cna {bio3d}

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 class 'cna'
print(x, ...)
  ## S3 method for class '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.

Details

Simple summary and print methods for protein dynamic networks.

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.

Author(s)

Guido Scarabelli and Barry Grant

References

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

See Also

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

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)

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

detach(hivp)

}