Convert a symmetric matrix to JSON for use with the Checkerboard web application

mtx2json.py

#!/usr/bin/env python                                                                                                                                                              

import sys
import json

ct = {}
ct_a = []
ctr = 0
for line in sys.stdin:
    if ctr == 0:
        ct_a = line.strip().split('\t')
    else:
        elems = line.strip().split('\t')
        ct_k = elems[0]
        ct_vs = elems[1:len(elems)]
        ct_v_ctr = 0
        for ct_vi, ct_v in enumerate(ct_vs):
            if ct_v_ctr == 0:
                ct[ct_k] = {}
            try:
                ct[ct_k][ct_a[ct_vi]] = float(ct_v)
                if ct_a[ct_vi] not in ct:
                    ct[ct_a[ct_vi]] = {}
                ct[ct_a[ct_vi]][ct_k] = float(ct_v)
            except ValueError as ve:
                if ct_v == 'NA':
                    ct[ct_k][ct_a[ct_vi]] = None # encode NAs as 'null' in JSON output                                                                                             
            ct_v_ctr +=1
    ctr += 1

sys.stdout.write("%s\n" % (json.dumps(ct)))

Here's an example of a figure from the JSON string posted above:

An example of what the Checkerboard application looks like when adding data, selecting cell types (or samples), and ordering them before rendering a plot: