This plug-in loads an expression data file (consult the Cytoscape manual to learn
about the format of this type of file) and then allows the user to color the nodes
in a network according to their expression values. The GUI works like a VCR, with
play, pause, and stop buttons. If the user presses the play button, the plug-in will
iterate over all the conditions in the expression file and color the nodes according
to their corresponding expression values.
###Using the plug-in
The plug-in starts up with default minimum and maximum expression values: -1 and 1.
It colors nodes with a color ranging from blue to red, depending on the value
of their expression (blue hue if close to -1, red hue if close to 1).
To change the colors or the minimum and maximum expression values, press the icon
that looks like a multi-colored pie on the Cytoscape tool-bar (this is the Visual
Styles dialog). Then edit the current visual style. Look for the "dynamicXpr" Node
Color mapping, and you should be able to reset colors or add/remove points in the
continuous range of values. After making changes, you can run the plug-in, and you
will see the effects of your new settings.
Additionally, the plug-in assigns to each node at each condition a "significance"
attribute (if present in the loaded expression file). So, if you wish to map this
attribute to a visual node attribute, you can do so by creating a node visual
calculator (again, using the Visual Styles dialog) and then running the plug-in.
For example, some people like to map the significance to the node border thickness.