#acl All:read

= TIPS ON HOW TO USE ENRICHMENTMAP AND CYTOSCAPE (provided by the bioinformatics service) =
Description of the page:
 * this page collects tips on how to use EnrichmentMap and Cytoscape based on frequently asked questions and known issues. 
 * it is based from received feedback and tailored to the need of the OICR Cancer Stem Cell users (http://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cell)
 * do not hesitate to contact us if you need any assistance while executing these steps or have issues not reported on this page (veronique.voisin@gmail.com) 
 * for description on our workflow or how to create a maps, please visit these pages : http://www.baderlab.org/VeroniqueVoisin/Intranet/Protocol, http://www.baderlab.org/Software/EnrichmentMap

= TIPS SECTION START HERE: =

= Cytoscape 3.2 =
 * will be officially released soon, please wait for update
 * you can use this script to upgrade your cytoscape 2.8 session files:[[attachment:convert_cyto_28_to_3_EM.sh]] or use the manual procedure described in the Cytoscape 3.1.1 section

= Cytoscape 3.1.1 =

  * recommended version of EnrichmentMap is 2.0.1 (Sept 22, 2014)
  * runs on java 7

== Create a figure (manual annotation) with an EnrichmentMap in Cytoscape 3.1.1 [tips created on Sept 23, 2014] ==
  * How to create a figure with manual annotation of the functional modules (note: an automatic annotation function will be soon available for Cytoscape 3.2):
   1. Change the background to white: 
     * in Control Panel
       * --> Style
         * --> at the bottom, select Network
           * --> Background Paint: choose the white color and click on OK
   * remove the labels:
     * go to Table Panel
      * -> double check that you have the focus on Node Table
       * --> Click on the 5th Symbol item to create a "New Single Column" --> Integer
        * --> name this new column "no_labels"
     * go to Control Panel --> Style
       * make sure that the focus is on "Node" (at the bottom)
       * change Label --> Column to "no_labels" 
   * Export the network as a pdf:
     * arrange the nodes and the view as you would like them to appear on the figures (e.g red nodes on the left and blue nodes on the right)
     * Click on the icon "Export Image to File" 
       * --> choose the PDF format, browse to your desired folder, choose a name and click on "OK"
   * Open a powerpoint document and import the pdf file:
    * looking at the labels of single nodes or using the application WordCloud to look at the labels of a group of nodes, manually annotate the map on your powerpoint slide.
    
= Cytoscape 2.8 =

  * To use Cytoscape 2.8, Cytoscape 2.8.3 and version of EnrichmentMap 1.3 is recommended (Sept 23, 2014)
  * Cytoscape 2.8 runs with java6 only.
  * It is recommended to use the latest version of Cytoscape (Cytoscape 3) to get benefits from new features (unless you can't upgrade to java 7 or 8).
== If you have a project done with Cytoscape 2.8 and want to correctly open these files with Cytoscape 3 you can follow this procedure (recommended for experienced users only)(Sept 23, 2014): ==
=== How to make a Cytoscape 2.8 file compatible for Cytoscape 3 : ===
    * open Cytoscape 3.1.1
    * open the 2.8 file
    * save the file with a new name (e.g. _cyto3)
    * change the extension from .cys to .zip for both the old and new files
    * unzip the old and new files
    * copy the folder called Enrichment_Map_plugin (located in the plugins folder) from the old file to the Apps folder of the new file and call it EnrichmentMap (old cyto2.8 file/plugin/Enrichment_Map_plugin --> new cyto3 file/Apps/EnrichmentMap)
    * zip the new session with a new name and replace the extension .zip to .cys
     *zip -r DP_ImmGeneUP_nov18_2013_cyto3_emadded.zip  CytoscapeSession-2014_09_18-09_44
     *mv DP_ImmGeneUP_nov18_2013_cyto3_emadded.zip DP_ImmGeneUP_nov18_2013_cyto3_emadded.cys