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February 15, 2018 05:21
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Convert a symmetric matrix to JSON for use with the Checkerboard web application
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| #!/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:
- 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.
- 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.
- 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.
- Click on the "Render" button to render a plot.
- 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:
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Here's an example of a tab-delimited matrix, showing a grid of pairwise metrics (0 <= s[ij] <= 1) for some set of samples (cell types, etc.):
Here's the result of converting this matrix to JSON:
This string can be cut-and-paste into the Checkerboard application at: https://tools.altiusinstitute.org/checkerboard/