gps2xgmml {chroGPS} | R Documentation |
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.
gps2xgmml(x, fname='out.xgmml', names.arg, fontSize=4, col=gplots::col2hex('steelblue'), cex)
x |
Object of class |
fname |
Name of output file |
names.arg |
Names for each point. If missing, they're taken from |
fontSize |
Font size |
col |
Fill colour(s) for the plotting symbols. Should be given in
hexadecimal, e.g. as returned by function |
cex |
Expansion factor for plotting symbols. By default,
|
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.
Generates an .xgmml file that can be opened in Cytoscape (File -> Import -> Network).
#See help(mds) for an example