TIPS ON HOW TO USE ENRICHMENTMAP AND CYTOSCAPE (provided by the bioinformatics service)
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 an issue not reported on this page (veronique.voisin@gmail.com)
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:convert_cyto_28_to_3_EM.sh or use the manual procedure described in the Cytoscape 3.1.1 section
Cytoscape 3.1.1
- Sept 22, 2014:
recommended version of EnrichmentMap is 2.0.1
- 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):
- Change the background to white:
- in Control Panel
--> Style
--> at the bottom, select Network
--> Background Paint: choose the white color and click on OK
- in Control Panel
- 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"
- go to Table Panel
- 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.
- Change the background to white:
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 (recommended for experienced users only):
- * 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
- * How to make a Cytoscape 2.8 file compatible for Cytoscape 3: