Arranging meta nodes into a circular layout in Cytoscape
Entering edit mode
19 months ago


I did clustering of enrichment terms in cytoscape (1. Used ranked list used to run gProfiler, 2. Used clustermaker2 to cluster the similar terms., 3. Used auto annotate to annotate the clusters., 4. Used enrichmentmap to visualize the clusters., 5. Used groups attribute layout to get the visual output below). I largely depended on the script provided here as part of this research article ((Gary Reynolds et al.; Science 2021.)). enter image description here

So now I have meta nodes where each meta nodes are clusters. I tried all the layout options in different way to obtain a figure as seen in this publication (Gary Reynolds et al.; Science 2021.) as below However, I could not 'circularize' my meta nodes as is seen in the publication (Apart from selecting each meta node and dragging manually to arrange in circles).

enter image description here

What I already tried is also the summarizing option.If I summarize, I obtain the meta nodes as single nodes but do not show any more the details of sub nodes. Then I use yFiles circular layout to obtain this enter image description here

Then, I used the copycat layout feature to copy the layout style of this summary network to obtain the circular arrangement of unsummarized netwrok, but didn't work as I hoped. Again, no sub nodes displayed as in the publication. enter image description here

Is there anything obvious I am missing? Can anyone help?

circular cytoscape enrichmentmap analysis layout network • 944 views
Entering edit mode
19 months ago
mikekucera ▴ 10

Hi, Unfortunately there is no circular layout for compound nodes in Cytoscape or AutoAnnotate. You will have to manually arrange the clusters in a circle.


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