chroGPS (version 1.16.0)

gps2xgmml: Export an 'mds' object to Cytoscape .xgmml format

Description

gps2xgmml creates a .xgmml file for visualizing MDS results in Cytoscape. Two-dimensional MDS maps can be visualized in Cytoscape as usual. For three-dimensional maps Cytoscape's 3D Renderer (http://wiki.cytoscape.org/Cytoscape_3/3D_Renderer) is required.

Usage

gps2xgmml(x, fname='out.xgmml', names.arg, fontSize=4, col=col2hex('steelblue'), cex)

Arguments

x

Object of class mds

fname

Name of output file

names.arg

Names for each point. If missing, they're taken from x.

fontSize

Font size

col

Fill colour(s) for the plotting symbols. Should be given in hexadecimal, e.g. as returned by function col2hex from gplots. Tips: col2hex('steelblue') looks nice in 2D/3D plots, col2hex('steelblue') looks nice in 2D plots and a bit faded on 3D plots.

cex

Expansion factor for plotting symbols. By default, cex=12 for 2D plots and cex=100 for 3D plots.

Value

Generates an .xgmml file that can be opened in Cytoscape (File -> Import -> Network).

Details

The .xgmml file contains the map co-ordinates in 2 or 3 dimensions, depending on the number of dimensions stored in the input mds object. To visualize properly a file with 3D co-ordinates, you need to install Cytoscape's 3D Renderer (http://wiki.cytoscape.org/Cytoscape_3/3D_Renderer) and start Cytoscape following the instructions provided therein. An .xgmml file with 3D co-ordinates can still be visualized in regular Cytoscape but the z-axis will be ignored.

Examples

#See help(mds) for an example