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Arcadia-Science / sourmashconsumr

Working with the outputs of sourmash in R
https://arcadia-science.github.io/sourmashconsumr/
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for `plot_taxonomy_annotate_ts_alluvial()`, add a `show_tax` argument that allows the user to control which taxa are given alluvial ribbons #40

Open taylorreiter opened 2 years ago

taylorreiter commented 2 years ago

motivated by a suggestion by @elizabethmcd in #37 and inspired by show_tax in ampvis2 https://kasperskytte.github.io/ampvis2/articles/ampvis2.html

How the function works right now is it uses a fraction_threshold (by default, 0.01, or 1%) -- if a lineage is present in any of the time series at 1% or greater, it gets an alluvial ribbon in the plot. The user can change the fraction_threshold to anything they want it to be. Anything that does not get an alluvial ribbon gets automatically clumped into "other" via a process implemented in the function.

I like the idea of tax_show. This would allow users to either provide a list of taxa to tax_show or use fraction_threshold.