Visualize assembly graph of selected contigs

[evanroyrees]

Kind of like bandage mixed with current plots

Use would be to determine HGT and resolve contigs with highly different coverage

[evanroyrees]

Currently cytoscape component is in refactor branch

contig cytoscape component

This is crude at the moment and probably not all that helpful to the user. Some additional information should be displayed alongside some other tools to help with interaction, style, etc.

Some ideas for further progress:

1. script to create cytoscape connections table that will be required as input for this component

This script would require two input groups (1. metagenome assembly, 2. metagenome reads)

• reads are mapped to metagenome assembly
• mapped reads checked for connections along starts and ends of contigs

2. Ability to choose different layout configurations based on user preference
3. Change behavior based on whether has provided connections table or condensed connections table.
4. Default request should be the connections table as this has connection to the contig's start or end information available allowing for a directed graph to be constructed. The directed graph would be more informative than simply displaying connections between contigs
5. Currently the size of the edges between nodes is weighted by the number of connections while also displaying the number of connections as an edge annotation... This is bulky, distracting and should this behavior should be removed from the styling
6. Selections only display two colors denoting contigs selected vs. connected contigs that were not selected. Ideally the colors would correspond to the colors displayed in the 2D scatterplot that were selected
7. Styling should be implemented to denote between the start and end contig connection

There are likely more here that I'm missing or forgetting but ideally getting some user feedback would be preferred after these are implemented.

[evanroyrees]

#39 merged some minimum working code for this. Sample ingestion of cytoscape.connections.tab currently gets killed in docker container. Greater resources should resolve this.