Thursday, 1 October 2015

Chord diagrams: when there’s too many categories to Venn!

At the moment I’m comparing differentially-expressed genes from six different transcriptome studies. With this many categories, graphically representing cross-study commonalities is challenging. Chord diagrams are visually appealing, and provide several advantages over the tradition Venn:

Venn diagrams 
  • Gene lists are represented as shapes
  • List representation is not proportional to list size (although Eulerian circles can do this)
  • Common elements (shared gene findings) are shown by shape intersection
Chord diagrams
  • Gene lists are represented as annulus segments (with larger segments indicating more implicated genes)
  • Common elements (shared gene findings) are represented by the lines connecting two segments
  • This allows emphasis of important commonalities (e.g. lines are shown in colour when two gene lists contain statistically significant overlap)

Creating a Chord diagram

Using NetworkAnalyst you can create a Chord diagram within a few minutes.
  1. Choose the ‘starting with gene or protein lists’ module
  2. Upload your gene lists
  3. Choose ‘chord diagrams’
  4. Save the image as an .svg so you can edit it in Illustrator (or freeware vector editing software)
Sometimes the .svg saved from NetworkAnalyst will crash Illustrator. If this happens, open the svg in notepad and delete the extraneous text between ‘<style type=’ and ‘</style>’. When you then open the svg in Illustrator, the lines of the cord diagram may also have fill (making the centre a solid colour). If this happens set the fill to null for all lines in the middle of the cord diagram.
  1. Click somewhere in the middle of the cord diagram
  2. From the top menu, choose ‘select/same/fill colour’. This should select everything in the centre of the diagram, and leave the annulus and text unselected
  3. In the colour window, change the fill colour to null (leaving only a stoke colour). For help using the colour tool see my earlier post
  4. Add the finishing touches to the diagram (labels, colour scheme etc)