In Higashi, we also implemented a visualization tool which helps the users enjoy Higashi better. The visualization tool allows interactive navigation of the scHi-C analysis results and is implemented based on bokeh.

Configure Higashi-vis

Higashi-vis is really easy to configure. First, create a visual_config.JSON file under the directory config_dir. The directory structure should be

 .
 ├── Higashi
 │   ├── higashi
 │   └── config_dir
 └──     └── visual_config.JSON

The visual_config.JSON file should have the following content:

{
  "config_list": [
    PATH1,
    PATH2,
  ]
}

where PATH1, PATH2 is the path to the Higashi configuration files that is created before (See details here)

Launch the service

After configuring the parameters, just run the following commands

cd higashi
bokeh serve --port={PORT} --address=0.0.0.0 --allow-websocket-origin=*:{PORT} Higashi_vis/

If more than one user would be visiting the site at the same time, please also include --num-procs {NUM} here such that the server can handle multiple process at the same time. See details about the bokeh server here

Finally, open a browser and go to {IP}:{PORT}/Higashi_vis. If you are running the program with a PC, the {IP} can just be localhost. If you are running this on a server, {IP} would be the ip address of the server. Notably, the server itself should allow the accession of this {PORT}. If you see the following interface, you have successfully launched the visualization tool.

Note: Higashi-vis will be updated with more features. So the interface could change frequently. Please raise an issue if you have any questions and suggestions about Higashi-vis.

Navigate the analysis results

See here for details.

Warnings: There are a lot of gifs for detailed instructions. It could take some time to load the whole page depending on the network you are using. Also, the size of the gifs are not friendly for mobile user. Please browse the page on devices with large screens.