Related Issues (20)
- Add command-line options to the SPE script to control the embedding
- Show the number of search terms found.
- Write a script to update metadata of data points/clusters
- Take care of licencing
- Improve search functionality
- Optimize SPE
- Unit tests & Code doc
- Hierarchical embedding - estimate distances that are not given
- User-defined colours for background and selected data points
- Compare OMAViz to Cytoscape 3.4.0
- Compare the spatial embeddings obtained from different kinds of protein similarity networks
- Add option to SPE to filter similarities/distances
- normalize similarity scores
- Check if the input matrix contains similarities or distances
- Add option to compute either 2D or 3D embedding
- Establish the relationship between the input similarities/distances and radius of the spherical embedding
- Exceptions handling
- Use min-max normalization for input graphs with PAM distances
- Missing self-similarities in Candy gene data
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