dynamicXpr

Dynamically change colors of nodes like a movie according to their expression level across many conditions.
(2)
###Introduction 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.
CYTOSCAPE 2

Version 1.3

Released 18 Sep 2008

Works with Cytoscape 2.6

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