#acl All:read <> = TIPS ON HOW TO USE ENRICHMENTMAP AND CYTOSCAPE (provided by the bioinformatics service and EnrichmentMap software developpers) = 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 from 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 STARTS HERE: = = Cytoscape 3.2 = * runs on java7 * java7 is installed by default on (recent) Windows machines but not on MAC machines which run java 1.6 by default. * To install java 7, you don't need to uninstall java 6 first; * Once you installed java 7,open your terminal window and type "java -version"; if the terminal tells you java version "1.6.x_xx", you may type this command "export JAVA_HOME=$(/usr/libexec/java_home -v 1.7)" to run java 7 * see instructions here: [[http://baderlab.org/InstallingCytoscape32OnMacOSXSnowLeopard | here ]] if you have an older Snow Leopard 10.6.8 and need to upgrade to java 7 * 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 * the recommended enrichmentmap version for Cytoscape 3.2 is the enrichmap version that contains the automatic annotation option (Release 2.1.0 ) * more on java folders and set JAVA_HOME environment variable to Java 7 path: *https://developer.apple.com/library/mac/qa/qa1170/_index.html == How to collapse group nodes into a single metanode (in order to simplify the map) == * use cytoscape 3.2.1 or later and latest EnrichmentMap version (built 627 or later) * manual creation of groups and manual collapsing of nodes (1 by 1) * create a group of nodes: * select nodes to form a group * right click on the selected nodes and choose the option "group" ==> "group selected nodes" ==> name it * double click on the group on the node to collapse it. * to expand a metanode, double-click on it and the individual nodes forming the group will be displayed. * automatic options * add automatic labels using the "Annotate Cluster" feature (in menu --> EnrichmentMap --> Annotate Cluster) * run the "Annotate Cluster" with the option "Create Groups for clusters" checked (Control Panel --> Annotation Panel --> Advanced Option --> Create Groups for clusters). * Collapse all the groups: * menu bar ==> Tools ==> Command Line Dialog * type: group collapse grouplist ="all" * examples of help commands * help group * help group collapse * once the metanodes are created, we can change their size, color , shapes as other nodes. We also can import attributes for these nodes. == How to create a signature gene-set to use with the post-analysis option of enrichmentmap == * take the list of genes that you want to overlap with the map * make sure the gene identifiers of your list is the same as the ones used to create the enrichmentmap (e.g Gene Symbol) * open a new Excel workbook and transform the cell format to test (menu --> format --> cell --> text) * leave the first 2 column emptys and paste using the special/ transpose option to paste your gene list horizontally on the Excel worksheet (first line) * give a name and description of your list in the first 2 columns * save it as a tab delimited file and then change the extension from .txt to .gmt * once your gene signature .gmt file has been created, you can follow this protocol: * http://baderlab.org/Software/EnrichmentMap/PostAnalysisTutorial == Modify the node size to be proportional to GSEA NES (normalized enrichment score) == * red nodes have NES with positive values and blue nodes have NES with negative values * Go to Control Panel --> Style -- Size --> expand the right arrow * in Column, change EM1_gs_size_dataset1 to EM1_NES_dataset1 * double-click on the current mapping diagram (blue and white rectangle) * set the min and max to -3 and 3 respectively * add 2 tabs using the "Add" button and set the new tabs to 1.4 and -1.4 and the x axis * on the y axis, set the nodes values to * 65 for -3 * 25 for -1.4 * 25 for 1.4 * 65 for 3 * click on "OK" to apply the changes {{attachment:modifyNES.png}} = Cytoscape 3.1.1 = * recommended version of EnrichmentMap is 2.0.1 (Oct 5, 2014) * runs on java 6 or 7 == Open an existing enrichment map session file (.cys) (Oct 5, 2014) == * to fully open a stored session: open Cytoscape first and then the session file. == Create a figure (manual annotation) with an EnrichmentMap in Cytoscape 3.1.1 [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. == Move label position of nodes (Oct 5, 2014) == * go to Style in the Control Panel and click on the word "Properties" (it gives a list of all properties) * --> choose "Label Position" (this property is now added to the list) and double click on the first box (icon with a rectangle box) to move the labels to desired position) *{{attachment:label_position.png}} == Change Edge Color (Nov 14, 2014) == * go to "Style" in "Control Panel" and chose at the bottom the "Edge" Panel. * Look for "Stroke Color (Unselected)" and click on the arrow (right) to expand the panel * click on a colored rectangle to change the color. By default, green is for dataset 1 and blue is for dataset2 in the case that you created a map with 2 datasets. * {{attachment:edge_color.png}} = Cytoscape 2.8 = * To use Cytoscape 2.8, Cytoscape 2.8.3 and version of EnrichmentMap 1.3 is recommended (Sept 23, 2014) * 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)(tips created on 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