Comments (2)
It should be possible for the user to specify a range of components, instead of just a boolean "all or one" thing. Enclosed are some sample "inputs" and what should be displayed:
- 2
- renders just component 2 (this is the only sort of input the viewer interface accepts at present).
- 1–3
- renders all components from rank 1 to rank 3, inclusive.
- 1, 4, 5
- renders components 1, 4, and 5.
- all
- renders all components in the graph.
- all WHERE number_nodes >= 3
- renders all components in the graph where the number of nodes is greater than or equal to 3.
- implementing this will necessitate running some sort of query through sql.js to identify the exact component IDs involved; allowing the user to provide the literal SQL queries themselves might make implementing this a bit easier, although that'd 1) necessitate user expertise with SQL and the .db structure and 2) be really insecure, so I don't think it's the best idea here.
- 1, 2, 5–8
- renders components 1, 2, and all components in the inclusive range of 5 to 8.
The latter two input types are really fancy (but, of course, potentially really useful -- esp. the second-to-last input type) and I'm not even sure how to efficiently implement them off the top of my head, so I think working towards input cases 2, 3, and 4 above is probably a sufficient goal for the time being.
from metagenomescope.
Planned options:
- Draw single component (current behavior -- shows a single component selector)
- Draw component containing a node (shows a text box the user can enter a node name in; will draw this component, if present)
- Draw range of components (shows two component selectors, one labeled
from
and another labeledto
, and draws all components in that range). - Draw all components (doesn't have any extra UI elements -- just a button that draws all components)
Number 3 might be difficult (mostly from a UI perspective tbh), but 2 and 4 shouldn't be too bad to do with the new data handling stuff (and I think they'll be the most useful).
from metagenomescope.
Related Issues (20)
- Prevent long node labels from extending past pattern boundaries
- Change the "chain" color to something more neutral HOT 1
- New type of pattern: bipartite subgraphs HOT 1
- Better component tiling
- Aggregate some statistics in node / edge tables
- Add "select all" option
- Blurry exported screenshots HOT 1
- Automatically cropping screenshots HOT 1
- Pass PATTERN2COLOR from Python to JS?
- Allow searching to return complements if needed
- Thicken duplicate edges HOT 1
- [Feature Request] Output a graph file that could be used elsewhere (e.g., NetworkX, iGraph, or Cytoscape) HOT 4
- Compress main.js more
- Pass extra GFA segment / link attributes (tags) to the visualization
- Support duplicate (aka parallel) edges in GFA / FASTG files?
- Draw arrowheads in both directions for self-implying edges
- Identifying cyclic bubbles? HOT 1
- Identify cyclic frayed ropes?
- Support general node / edge metadata
- Adjust max node / max edge counts to consider the top layer of the decomposed graph
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from metagenomescope.