# Contact Map Chord Diagram Plotting¶

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 """ Simple contact cmap Chord plotting ================================= This script contains a simple example of how you can plot contact cmaps in Chord Diagram style using ConKit """ import conkit.io import conkit.plot # Define the input variables sequence_file = "toxd/toxd.fasta" sequence_format = "fasta" contact_file = "toxd/toxd.mat" contact_format = "ccmpred" # Create ConKit hierarchies # Note, we only need the first Sequence/ContactMap # from each file seq = conkit.io.read(sequence_file, sequence_format).top conpred = conkit.io.read(contact_file, contact_format).top # Assign the sequence register to your contact prediction conpred.sequence = seq conpred.set_sequence_register() # We need to tidy our contact prediction before plotting conpred.remove_neighbors(inplace=True) conpred.sort('raw_score', reverse=True, inplace=True) # Finally, we don't want to plot all contacts but only the top-L, # so we need to slice the contact cmap cmap = conpred[:conpred.sequence.seq_len] # Then we can plot the cmap fig = conkit.plot.ContactMapChordFigure(cmap, legend=True) fig.savefig("toxd/toxd.png") 

Each residue in the Chord plot corresponds to an amino acid in your sequence. For a full list of the encoding used, check the ContactMapChordFigure.

The color coding of the full sequence used is the following:

Q P R R K L C I L H R N P G R C T Y D K I P A F Y Y N Q K K K Q C E R F D W S G C G G N S N R F K T I E E C R R T C I G