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gtonkinhill / Efcm_Efcs_analysis

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cytoscape figure #1

Open smb20200615 opened 2 years ago

smb20200615 commented 2 years ago

Hello,

I am interested in the output of your network analysis and so I loaded the edges csv file that you provided into cytoscape but couldn't reproduce the figure from your paper - the distinct clusters from your manuscript figure looked like one big cluster. I loaded the three column file as "source", "target", and "edge attribute". I then selected the organic layout. I was wondering how I can arrive at the figure from your manuscript. Perhaps you pruned the edges further prior to loading to cytoscape? Apologies if I am mistaking.

Thanks

gtonkinhill commented 2 years ago

Hi,

We performed the edge filtering within Cytoscape such that edges had a weight ≥0.95 indicating that isolates shared ≥95% of their accessory genome.

In case it is helpful, the filtering functionality in Cytoscape is described here

Hopefully this helps and please let me know if you have any other questions.