sonjageorgievska / omaviz Goto Github PK
View Code? Open in Web Editor NEWVisualization of the data of the Candy Gene project
Home Page: http://sonjageorgievska.github.io/OMAViz/
License: Other
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omaviz's Issues
Check if the input matrix contains similarities or distances
Improve search functionality
Check the integrity of input data
Cluster members without similarity data should not be displayed
Show/hide the tooltip on click rather than on hover event
Hierarchical embedding - estimate distances that are not given
Exceptions handling
Add try/catch exception handlers to notify user of missing input files in the python and the javascript code.
See if (in the front end code) some missing input files can be tolerated.
User-defined colours for background and selected data points
Optimize SPE
Compare the spatial embeddings obtained from different kinds of protein similarity networks
Write a script to update metadata of data points/clusters
Show the number of search terms found.
Make the SPE script compatible with Python2/3
Add command-line options to the SPE script to control the embedding
Take care of licencing
Establish the relationship between the input similarities/distances and radius of the spherical embedding
Add option to compute either 2D or 3D embedding
Use min-max normalization for input graphs with PAM distances
Compare OMAViz to Cytoscape 3.4.0
Input data: MUSAC-MUSAM.graph with 71,458 nodes and 2,200,051 edges
Data dimensionality: OMAViz (3D) Cytoscape (2D)
Interactvity/performance: OMAViz (+) Cytoscape (-)
Search: OMAViz (+) Cytoscape (-)
Missing self-similarities in Candy gene data
For example, we don't have the self similarity of SOLLC19749
Add function to select/hide data points
normalize similarity scores
Unit tests & Code doc
Add option to SPE to filter similarities/distances
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