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pogorely / reverse_epitope_discovery

Data and code for Rosati, Pogorelyy, Minervina et al 2021.
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Fig 2D. Epitope Discovery - Graph Network #2

Open drEast opened 1 year ago

drEast commented 1 year ago

Hi, Thanks for this amazing work. Really exciting to see that these TCR distances also work in practice. I tried to recreate the TCR clonotype network from Figure 2D, since I ultimately want to apply a similar analysis to my own data. I was able to reconstruct the Network Graph reasonably well on your data. Could you please explain how you derive the visualization from there via the Gephi tool mentioned in the Paper? Thanks for your help. Best, Felix

pogorely commented 1 year ago

Hi Felix,

1) save network to the file using igraph: write_graph(grb_filt, file=“my_network.gml , format=“gml”) 2) open in Gephi, do "Force Atlas 2" layout (Layout pane -> Force Atlas 2 -> Run) 3) Filter singletons(optional) (Filters pane -> Topology -> Degree range -> move slider to Degree>0) 4) make node size proportional to the degree (Appearance pane -> Nodes -> Size -> Ranking -> set to "Degree") 5) color the nodes by the attribute of choice (Appearance pane -> Nodes -> Color -> Partition -> set to "mira_match")

Then you could export to pdf. Hope that helps!

Best, Misha

drEast commented 1 year ago

Hi Misha, Thanks that was very helpful. Best, Felix