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)))

Checkerboard overview:

1. Once you paste the JSON string into the Import column of the Checkerboard app, click on the "Import" button to bring it into the application.
2. In the Categories column, click on the "Select All" button to select all the cell types. Deselect any you don't want by clicking on their checkboxes.
3. In the Ordering column, drag-and-drop the "hamburger" symbol next to each cell type up or down, to re-order the cell-types as desired.
4. Click on the "Render" button to render a plot.
5. In the "Figure" column, click "Export" to export a plot to an SVG file. This can be imported into Adobe Illustrator or Inkscape.

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: