Add sampling year coloring #12
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For builds where we've chosen not to infer a timetree it's still very useful to communicate the sampling date. Here we export the year which forms a nice continuous coloring. (An ordinal coloring would be better but the date range in this dataset means Auspice repeats colors which isn't ideal. Temporal coloring will be better once it accepts YYYY-MM-DD strings, but as of Auspice 2.55 it interprets integers as January 1st.)
Not yet exported as a coloring (year is preferable, see previous commit) but this allows the sampling date to appear when clicking on tips and as a filtering option.
genehack
approved these changes
Aug 22, 2024
joverlee521
reviewed
Aug 22, 2024
| @@ -30,7 +31,7 @@ rule export: | |||
| --tree {input.tree} \ | |||
| --metadata {input.metadata} \ | |||
| --metadata-id-columns {params.strain_id} \ | |||
| --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \ | |||
| --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} {input.year} \ | |||
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not asking for a change, just curious
Instead of making another node-data JSON, why not just add a year column to the metadata.tsv that can be used directly as a coloring?
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I found the approach here cleaner to implement, although if other rules used the data I'd have probably gone for modifying the TSV. It should also be trivial to copy & paste into other workflows which would benefit from this. Of course, once Auspice has a proper temporal scale this'll all be removed anyways.
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Perhaps analogous to avian-flu where we currently add in a column (H5 LABEL) to the TSV but want to switch away from this to a node-data JSON
kimandrews
approved these changes
Aug 22, 2024
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For builds where we've chosen not to infer a timetree it's still very useful to communicate the sampling date. Here we export the year which forms a nice continuous coloring. (An ordinal coloring would be better but the date range in this dataset means Auspice repeats colors which isn't ideal. Temporal coloring will be better once it accepts YYYY-MM-DD strings, but as of Auspice 2.55 it interprets integers as January 1st.)
We also export the date string, which is shown when clicking on tips is available as a filtering option.