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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.
GNU General Public License v3.0
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Visualizing results #74

Closed underbais closed 6 years ago

underbais commented 6 years ago

I am trying to use your package PhyloWGS and I am stuck with step 5. View results.

I am running it in the cluster so there is no way I can initiate a browser like you specify at Github https://github.com/morrislab/phylowgs

So, is there other ways to visualize results using your package to get the trees?

Thanks

jwintersinger commented 6 years ago

You have several options:

  1. Run write_results.py and transfer the resulting files to your local machine, then run Witness from there.
  2. Use something like SSHFS (https://github.com/libfuse/sshfs) to mount the cluster's filesystem locally, and again run Witness from your local machine.
  3. Set up an SSH tunnel (e.g., ssh -L 8000:localhost:8000 user@example.org). This way, you can run a web server on the cluster (via python2 -m SimpleHTTPServer), but still connect to it from your local machine.

Please let me know if you need any other help!

vivekruhela commented 5 years ago

Hi, I am trying to visualize results using the command: `` but I am getting empty dashboard. All the files are generated from example data and saved in data sub-folder of witness folder. I run that command twice or refresh it but still getting empty dashboard. Here are the logs and command:

vivekr@sarabhai:~/clone_evolution/phylowgs/witness$ python2 -m SimpleHTTPServer Serving HTTP on 0.0.0.0 port 8000 ... 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET / HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /css/dashboard.css HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /css/tree.css HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/stupidtable.min.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/state_manager.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/cluster_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/interface.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/tree_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/tree_viewer.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/tree_summarizer.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/tree_util.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/pop_vaf_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/util.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:05] "GET /js/witness.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:06:07] code 404, message File not found 127.0.0.1 - - [06/Jul/2019 10:06:07] "GET /favicon.ico HTTP/1.1" 404 - 127.0.0.1 - - [06/Jul/2019 10:06:37] "GET /data/index.json HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET / HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/state_manager.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/stupidtable.min.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/tree_viewer.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/tree_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/interface.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/cluster_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/tree_summarizer.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /css/dashboard.css HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /css/tree.css HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/tree_util.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/pop_vaf_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/util.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:29] "GET /js/witness.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:07:30] "GET /data/index.json HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET / HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /css/dashboard.css HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /css/tree.css HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/state_manager.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/stupidtable.min.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/cluster_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/interface.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/tree_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/tree_viewer.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/tree_summarizer.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/witness.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/tree_util.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/pop_vaf_plotter.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:22] "GET /js/util.js HTTP/1.1" 200 - 127.0.0.1 - - [06/Jul/2019 10:10:23] code 404, message File not found 127.0.0.1 - - [06/Jul/2019 10:10:23] "GET /favicon.ico HTTP/1.1" 404 - 127.0.0.1 - - [06/Jul/2019 10:10:25] "GET /data/index.json HTTP/1.1" 200 -

vivekruhela commented 5 years ago

An update I would like to add here. I have got some visualizations but the script is hanging badly and results are not static (i.e. changing). There are multiple plots for the same x and y label which is confusing also. I have attached the figure below: Screenshot_2019-07-09 PhyloWGS Witness(3) Screenshot_2019-07-09 PhyloWGS Witness(4) Screenshot_2019-07-09 PhyloWGS Witness(5) Screenshot_2019-07-09 PhyloWGS Witness(6)

sahilseth commented 4 years ago

How did you solve the empty dashboard issue?

sainadfensi commented 8 months ago

How did you solve the empty dashboard issue?

I encountered same issue and later learned that I need to put results folder inside the witness/data/ folder. Hope this will help.