plot.cna. bio3d 2.3-0

Usage

"plot"(x, pdb = NULL, weights=NULL, vertex.size=NULL, layout=NULL, col=NULL, full=FALSE, scale=TRUE, color.edge = FALSE,  interactive=FALSE, ...)

Arguments

x: A protein network graph object as obtained from the ‘cna’ function.
pdb: A PDB structure object obtained from ‘read.pdb’. If supplied this will be used to guide the network plot ‘layout’, see ‘layout.cna’ for details.
weights: A numeric vector containing the edge weights for the network.
vertex.size: A numeric vector of node/community sizes. If NULL the size will be taken from the input network graph object ‘x’. Typically for ‘full=TRUE’ nodes will be of an equal size and for ‘full=FALSE’ community node size will be proportional to the residue membership of each community.
layout: Either a function or a numeric matrix. It specifies how the vertices will be placed on the plot. See ‘layout.cna’.
col: A vector of colors used for node/vertex rendering. If NULL these values are taken from the input network ‘V(x$community.network)$color’.
full: Logical, if TRUE the full all-atom network rather than the clustered community network will be plotted.
scale: Logical, if TRUE weights are scaled with respect to the network.
color.edge: Logical, if TRUE edges are colored with respect to their weights.
interactive: Logical, if TRUE interactive graph will be drawn where users can manually adjust the network (positions of vertices, colors of edges, etc.). Needs Tcl/Tk support in the installed R build.
...: Additional graphical parameters for ‘plot.igraph’.

Description

Plot a protein dynamic network as obtained from the cna function.

Details

This function calls ‘plot.igraph’ from the igraph package to plot cna networks the way we like them.

The plot layout is user settable, we like the options of: ‘layout.cna’, ‘layout.fruchterman.reingold’, ‘layout.mds’ or ‘layout.svd’. Note that first of these uses PDB structure information to produce a more meaningful layout.

Extensive plot modifications are possible by setting additional graphical parameters (...). These options are detailed in ‘igraph.plotting’. Common parameters to alter include:

vertex.label:: Node labels, V(x$network)$name. Use NA to omit.
vertex.label.color:: Node label colors, see also vertex.label.cex etc.
edge.color:: Edge colors, E(x$network)$color.
mark.groups:: Community highlighting, a community list object, see also mark.col etc.

Value

Produces a network plot on the active graphics device. Also returns the plot layout coordinates silently, which can be passed to the ‘identify.cna’ function.

References

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

Note

Be sure to check the correspondence of your ‘pdb’ object with your network object ‘x’, as few internal checks are currently performed by the ‘layout.cna’ function.

Examples


# PDB server connection required - testing excluded

require(igraph)

Loading required package: igraph
Loading required package: methods

Attaching package: ‘igraph’

The following object is masked from ‘package:bio3d’:

    gnm

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following objects are masked from ‘package:testthat’:

    %>%, compare

The following object is masked from ‘package:base’:

    union


##-- Build a CNA object
pdb <- read.pdb("4Q21")

  Note: Accessing on-line PDB file

modes <- nma(pdb)

 Building Hessian...		Done in 0.069 seconds.
 Diagonalizing Hessian...	Done in 0.284 seconds.

cij <- dccm(modes)


  |======================================================================| 100%

net <- cna(cij, cutoff.cij=0.2)

# Plot coarse grain network based on dynamically coupled communities
xy <- plot.cna(net)

Obtaining estimated layout with fruchterman.reingold

#plot.dccm(cij, margin.segments=net$communities$membership)

# Chose a different PDB informed layout for plot
plot.cna(net, pdb)


Obtaining layout from PDB structure



# Play with plot layout and colors...
plot.cna(net, layout=layout.mds(net$community.network), col=c("blue","green") ) 




# Plot full residue network colored by communities - will be slow due to number of edges!!
plot.cna(net, pdb, full=TRUE)

Obtaining layout from PDB structure



# Alter plot settings
plot.cna(net, pdb, full=TRUE, vertex.size=3, weights=1, vertex.label=NA)

Obtaining layout from PDB structure

Author

Barry Grant and Guido Scarabelli

Protein Structure Network Plots in 2D and 3D.