Visualize PhyloWGS output as tree

[philsteinberg]

PhyloWGS Result visualization: https://github.com/uclahs-cds/pipeline-call-SRC

TO-DO:

• download witness folder to local device
• rename extension -muts.json to .muts.json and -summ.json to .sum.json (created a PR to in call-pipeline-SRC to fix this)
• redownload index_data.py to create index.json
• visualize tree in browser

  mv test_results /path/to/phylowgs/witness/data
  cd /path/to/phylowgs/witness
  gunzip data/*/*.gz
  python3 index_data.py
  python3 -m http.server
  # Open http://127.0.0.1:8000 in your web browser. Note that, by
  # default, the server listens for connections from any host.

• Sort by negative log likelihood (select smallest)

[philsteinberg]

index_data.py File does not exist in witness folder. That script generates index.json, which is in the data folder. I copied index_data.py from the PhyloWGS github into my local witness folder and ran it to re-generate the index.json. That file is also an empty dictionary. When looking at the code in index_data.py there seems to be an additional input .clusters.json which we do not generate.

Error when running python2 -m SimpleHTTPServer

Serving HTTP on 0.0.0.0 port 8000 ...
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET / HTTP/1.1" 200 -
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 58464)
Traceback (most recent call last):
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 293, in _handle_request_noblock
    self.process_request(request, client_address)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 321, in process_request
    self.finish_request(request, client_address)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__
    self.finish()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish
    self.wfile.close()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close
    self.flush()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /css/dashboard.css HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /css/tree.css HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /js/stupidtable.min.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /js/state_manager.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /js/witness.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:13] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:13] "GET /favicon.ico HTTP/1.1" 404 -
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 58475)
Traceback (most recent call last):
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 293, in _handle_request_noblock
    self.process_request(request, client_address)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 321, in process_request
    self.finish_request(request, client_address)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__
    self.finish()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish
    self.wfile.close()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close
    self.flush()
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
127.0.0.1 - - [19/Dec/2022 09:36:16] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:16] "GET /js/stupidtable.min.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:16] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:16] "GET /js/state_manager.js HTTP/1.1" 404 -

I tried running it on the cluster and there it opens the window but there is no data loaded. Looking into past witness issues on the PhyloWGS github now.

[philsteinberg]

python3 -m http.server try this instead of python2 command

[philsteinberg]

Example: Witness data for sample ILHNLNEV000008-T001-P01-F and seed 97782

We create 2500 trees and choose the best tree (one that minimizes negative log likelihood (nlgLH))

Key & Interpretation:

• SSMs = Simple Somatic Mutations
• CNAs = Copy Number Abberations
• VAF = Variant Allelic Frequency
• Node = represents cancerous population
• CCF = Cancer Cell Fraction
• Color = represents subclone node arose from
• Number = Order of nodes by num of mutations (SSMs & CNAs)

Interpretation:

• 3 cancerous populations
• All nodes arise from same subclone (monoclonal)
• For node 1, 100% and for node 2, 38.7% of the tumor population harbor the mutation
• Node 2 has majority of SSMs and CNAs

Sample ILHNLNEV000004-T001-P01-F errored for some seeds. When visualizing this sample with seed 97782 all trees only have 2 nodes.

Sample ILHNLNEV000006-T001-P01-F and seed 97782