R: Protein Structure Network Layout

layout.cna {bio3d} | R Documentation

## Protein Structure Network Layout

### Description

Determine protein structure network layout in 2D and 3D from the geometric center of each community.

### Usage

      layout.cna(x, pdb, renumber=TRUE, k=2, full=FALSE)

### Arguments

`x` | A protein structure network object as obtained from the ‘cna’ function.
`pdb` | A pdb class object as obtained from the ‘read.pdb’ function.
`renumber` | Logical, if TRUE the input ‘pdb’ will be re-numbered starting at residue number one before community coordinate averages are calculated.
`k` | A single element numeric vector between 1 and 3 specifying the returned coordinate dimensions.
`full` | Logical, if TRUE the full all-Calpha atom network coordinates will be returned rather than the default clustered network community coordinates.

### Details

This function calculates the geometric center for each community from the atomic position of it's Calpha atoms taken from a corresponding PDB file. Care needs to be taken to ensure the PDB residue numbers and the community vector names/length match.

The community residue membership are typically taken from the input network object but can be supplied as a list object with 'x$communities$membership'.

### Value

A numeric matrix of Nxk, where N is the number of communities and k the number of dimensions requested.

### Author(s)

Guido Scarabelli and Barry Grant

### See Also

`plot.cna`, `plot.communities`, `igraph.plotting`, `plot.igraph`

### 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 will be slow
    #xy <- plot.cna(net)
    #plot3d.cna(net, pdb)

    layout.cna(net, pdb, k=3)
    layout.cna(net, pdb)

    # can be used as input to plot.cna and plot3d.cna....
    # plot.cna( net, layout=layout.cna(net, pdb) )
    # plot3d.cna(net, pdb, layout=layout.cna(net, pdb, k=3))

    detach(hivp)

    }

[Package bio3d version 2.3-3 Index]