gps2xgmml {chroGPS} | R Documentation

## 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=gplots::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.

### 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.

### Value

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

### Examples

    #See help(mds) for an example

[Package chroGPS version 2.4.0 Index]