Saw this figure from vdjdb-db github. https://github.com/antigenomics/vdjdb-db/tree/2017-03-18
It’s useful to show the connections among CDR3s and antigen epitopes but how to make this plot?


Firstly I’d like not note that this graph was made mainly for aesthetic purposes. The graph was visualized in Cytoscape, the edges and nodes were assigned as follows:

  • All epitopes like CMV-NLV were added as nodes
  • All CDR3 amino acid sequences were also added to the plot together with edges connecting them to the epitopes they recognize
  • CDR3 sequences that differ by no more than 3 (as far as I remember) substitutions were connected with edges

Thanks for sharing! I would love to have a try!