Showing Gene Annotations in an ODGI Matrix is a critical use case, but what that would even mean requires some thought. A single gene entry is not guaranteed to be entirely contiguous because different individuals can disagree on ordering of nodes.
Use Cases:
Choose one gene, generate a subgraph matrix for that one gene
Choose a region according to REF path.
Union of all available annotations into one track for pangenome
In both cases:
Pull in neighboring loci nodes
Sort optimally for this local area
Fragments of an annotation sorted into a distant x value will still have a clickable link back to the main body. This is good, though it's better if it never comes up.
Variation nodes inside of a gene annotation will be unannotated, but it should be clear from context the annotation is relevant.
Rendering Annotations
Tubemap does not have any intrinsic support for annotations
Each feature could be treated like a read, able to start and stop within nodes. Unfortunately, we're already making reads work double time.
Single canonical annotation is easiest to think about though only 90% honest
Best if we could piggyback synchronization on another browser that already renders annotation tracks
Requires expanding coordinate frame dynamically depending on pan-genome coordinate sizes
Could generate a new annotation track mapped to pan-genome coordinates to display in JBrowse
Showing Gene Annotations in an ODGI Matrix is a critical use case, but what that would even mean requires some thought. A single gene entry is not guaranteed to be entirely contiguous because different individuals can disagree on ordering of nodes.
Use Cases:
In both cases:
Rendering Annotations