#acl All:read

= TIPS =
 * this page collects tips on how to use EnrichmentMap and Cytoscape based on frequently asked questions and known issues.
 * it is based on feedback received from OICR Cancer Stem Cell users (http://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cell)


= Cytoscape 3.1.1 =

 *Sept 22, 2014:
  * recommended version of EnrichmentMap is 2.0.1
== 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:
   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 =
 * Sept 22, 2104:
  * To use Cytoscape 2.8, Cytoscape 2.8.3 and version of EnrichmentMap 1.3 is recommended
  * 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:
   *