Cytoscape ExpressionData PlugIns
---------------------------------

I.  Introduction
================
This directory contains a copy of the Cytoscape ExpressionData plugins.

The ExpressionProfileViewer plugin allows a user to view expression profiles
for selected genes in a network across multiple conditions.

The ExpressionCorrelationViewer plugin allows a user to visualize the correlation
of gene expression vectors for genes in a network across expression datasets with
the average of the normalized vectors of selected genes.

II.  Installation Instructions
==============================

To use the ExpressionData PlugIns, you must first obtain a copy of Cytoscape, 
Version 1.1.  You can download a copy from:  http://www.cytsoscape.org.  
Once you have downloaded Cytoscape and verified that it works, proceed with 
the next steps.  

1.  Copy the ExpressionData.jar file to your [Cytoscape_Home]/plugins directory.

2.  Load the plugin from the Cytoscape File/Open/Load plugin menu item or simply
    restart Cytoscape i.e. on Unix/Linux or MacOS X, run:

cytoscape.sh

On Windows, run:

cytoscape.bat

III.  Using the ExpressionData PlugIns
======================================

Once Cytoscape starts, select "PlugIns" from the Main Menu.  You will see two options
here:  "Expression Correlation Finder..." and "Expression Profile Viewer..."

ExpressionProfileViewer
1.  Load a network and associated gene expression data into Cytoscape from the file
    menu i.e. File --> Load --> Interaction...
              File --> Load --> Expression Matrix File...

    e.g. sampleData/galFiltered.sif and sampleData/galExpData.pvals

2.  Select genes of interest in the network.

3.  Select PlugIns --> "Expression Profile Viewer..."

4.  A window will pop-up showing you a plot of the expression profiles of the genes
    you have selected in the network across the gene expression conditions that you
    have loaded.

ExpressionCorrelationViewer
1.  Follow steps 1 and 2 from ExpressionProfileViewer

2.  Select PlugIns --> "Expression Correlation Finder..."

3.  A window will pop-up showing you a slider bar that allows you to view
    genes in the network that correlate with your selected genes at the given
    correlation level.  Further instructions are provided in the window.

4. A button on the pop-up enables you to additionally select the highly correlated genes. This selection can then be used as input to the Expression Profile Viewer above. Neither of these plugins "block" while active; that is, you may use any of the other features of Cytoscape while these plugins are operating.

V.  Bugs / Feature Requests
============================

If you encounter a bug with this PlugIn, or have a feature suggestion, we  
encourage you to use the Cytoscape Bug Tracker:
http://www.cbio.mskcc.org/cytoscape/bugs/.  

If you log a bug, we will automatically email you when the bug is resolved.

Known issues:

1. The labels of the experimental conditions are not displayed in the viewer.

2. The Expression Correlation Viewer manipulates the current visual style. Thus, you will experience problems if you attempt to switch visual styles or change the node coloring rules while this plugin is active.

VI.  Contacts
=============

Schwikowski Group, Institute for Systems Biology, Seattle
http://www.systemsbiology.org/

For any questions concerning this PlugIn, please contact:

Andrew Markiel: amarkiel@systemsbiology.org

This software is made available under the LGPL (Lesser General Public License).

This product includes the Visad library
(http://www.ssec.wisc.edu/~billh/visad.html).