Comments (2)
Currently cytoscape component is in refactor branch
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:
- 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
- Ability to choose different layout configurations based on user preference
- Change behavior based on whether has provided connections table or condensed connections table.
- 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
- 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
- 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
- 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.
from automappa.
#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.
from automappa.
Related Issues (20)
- Send in PR for Automappa bioconda recipe HOT 1
- Rename dashboard tabs
- After contig selection is saved, automatically hide saved contigs from view. HOT 2
- Provide summary stats of bins following extraction to fasta files
- Consider using same marker sets that CheckM uses to assess purity/completeness HOT 1
- Replace default page tab icon HOT 5
- Cache expensive callbacks HOT 1
- Refactor Scatterplot callbacks HOT 1
- Prevent scatterplots axes boundaries from changing on select/hide HOT 1
- Refinements table not displaying HOT 1
- Add metagenome and markers upload modal (or buttons or card, etc.)
- 🏠 Add home tab
- An approach to editing/removing/adding "vestigial" contigs from refined bins HOT 2
- 🐳 🍎 Docker image is not compatiblele with ARM processor
- Add notification to page when browser storage limits are reached
- problem installing HOT 6
- `Transferlist` for control of which clusters to keep/discard per sample
- The upload modal should tell you what the default filename should look like
- Add functionality to download figures
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from automappa.