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Arbitrary categorical / quantitative information associated with each node / edge. Something simple like TSV files would be sufficient. Maybe we have two optional parameters to the CLI (--node-metadata and --edge-metadata?), where each can refer to a TSV file where the rows are nodes / edges and the columns are metadata fields (e.g. TaxonomicClassification, Repetitive, ...)
The main purposes behind supporting this are:
Enabling the user to encode the visualization with this information -- i.e. node / edge colors, or edge thicknesses, or maybe node border colors (?), etc.
When we view information about a node / edge, show this information (along with existing node / edge properties, e.g. length, GC content, ...)
This information should probably just be stored in the same location as arbitrary GFA tag information (#238). We will need to do the standard sanity checking of "is the same metadata field name given in both files?", of course.
Support for this issue would supersede #8, #54, and #95. It isn't quite a replacement for #111, but I guess we could extend it to support #111 (I'll leave both this and #111 open for now).
Checklist
Python
Load node metadata; add it to graph, and then to visualization
Load edge metadata; add it to graph, and then to visualization
Check that metadata columns are not duplicated with other reserved names / etc.
JS
Implement arbitrary node coloring
Categorical
Quantitative
Implement arbitrary node border coloring
Categorical
Quantitative
Think really hard about if we want to support scaling node border thicknesses (mildly hot take: probably not)
Implement arbitrary edge coloring
Categorical
Quantitative
Implement arbitrary edge thickness scaling
Quantitative (there isn't a categorical analogue for this, right?)
Once this is ready, remove the Python scale_edges() stuff in favor of just letting the user scale edges by coverages in the JS (maaaaybe default to that, so that the default "workflow" for a user doesn't change)
The text was updated successfully, but these errors were encountered:
nice; i realize that duplicate node names are going to screw with
this, so i want to go through and double-check that the parsers all
reject graphs with duplicate node names
[ci skip]
Arbitrary categorical / quantitative information associated with each node / edge. Something simple like TSV files would be sufficient. Maybe we have two optional parameters to the CLI (
--node-metadata
and--edge-metadata
?), where each can refer to a TSV file where the rows are nodes / edges and the columns are metadata fields (e.g.TaxonomicClassification
,Repetitive
, ...)The main purposes behind supporting this are:
Enabling the user to encode the visualization with this information -- i.e. node / edge colors, or edge thicknesses, or maybe node border colors (?), etc.
When we view information about a node / edge, show this information (along with existing node / edge properties, e.g. length, GC content, ...)
This information should probably just be stored in the same location as arbitrary GFA tag information (#238). We will need to do the standard sanity checking of "is the same metadata field name given in both files?", of course.
Support for this issue would supersede #8, #54, and #95. It isn't quite a replacement for #111, but I guess we could extend it to support #111 (I'll leave both this and #111 open for now).
Checklist
Python
JS
scale_edges()
stuff in favor of just letting the user scale edges by coverages in the JS (maaaaybe default to that, so that the default "workflow" for a user doesn't change)The text was updated successfully, but these errors were encountered: