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)
Create a figure 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:
- 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: