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machina's Introduction

MACHINA Interactive Visualization

Akul Joshi, Vikram Ramavarapu

Overview of MACHINA

Installation and Setup

Installation and set up is very simple. Simply run the following commands:

cd machinaviz
npm install && npm start

You will then get the following return message:

Compiled successfully!

You can now view machinaviz in the browser.

  Local:            http://localhost:<port number>

In which case, simply open a browser and go to http://localhost:<port number>

Usage

Simply select a dataset and a patient ID to view the clonal trees and migration graphs. Clonal trees may have a dropdown for individual PMH Sankoff outputs if a clonal tree does not have a reported labelling. Migration graphs will have a dropdown menu as PMH has multiple solutions for any given clonal tree.

To switch to a different patient or dataset, simply deselect your current patient or dataset and switch to a new one.

User Interface of the visualization

machina's People

Contributors

vikramr2 avatar akuljos avatar

Watchers

 avatar

machina's Issues

Switch Graph Package to Multigraph Package

Our current package for tree visualization only allows for single edges in our graphs; however, due to the nature of polyclonal seeding, we need to switch to a graph library that allows for multiple edges from one node to another.

Fix Graph Ghosts

When switching between patients/directories, the graph from the previous patient/directory remains on the screen even when nothing is selected for the current patient. In addition, when the "-- Select labeling --" or "-- Select PMH --" options are selected, our program errors out with regard to the API calls.

Human Body Overlay

We want to overlay the migration graph selected by the user onto an image of the human body with the nodes representing certain anatomical sites placed accurately on the positions of those anatomical sites.

Fix Stuttering

When switching between different directories/patient records, there exists a little bit of stuttering before the graphs load, or the options in the directory/patient menus end up not being selected. Possible fix through transition to async/await structure?

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