How to change the size of the nodes in Cytoscape according to their relative abundance in co-occurrence network?
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9 months ago
dpc ▴ 170

Hi there!!! I am working with metagenomic sequence data. I have generated a species co-occurrence network from the species relative abundance data in Cytoscape. But in my network, all the nodes (species) are equal in size. I want to change the size of the nodes according to their relative abundance. How can I do that? Any suggestions?

thanks

cytoscape • 736 views
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9 months ago
zhangdengwei ▴ 140

You can upload a table offering two columns (name of nodes and their corresponding abundance). enter image description here

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9 months ago

Read the docs on styles. Apply a continuous mapping between abundance and node size following this tutorial (replace node color by node size).

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I have added a column to relative abundance table which contain sum of relative abundances of each taxa from all the subjects. Then imported it and done continuous mapping of "size" with "sum of relative abundances". Do you think this is a good way? Or should I calculate the mean value of abundances across samples and then do the mapping?

Thanks, dpc

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