Add visualizations for specific use cases like time series or different groups

[taylorreiter]

So far I've been focused on visualizations that will work no matter if samples are highly related, time series, different groups with lots of replicates, large or small sample sizes, etc. I think now that some of these base visualizations are encoded, I can do some more specific things as they come up.

Brainstorming below!

Time series

from: The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections. August 2017PLoS ONE 12(8):e0182520 DOI:10.1371/journal.pone.0182520

Differential abundance

Show in a vignette how to go from from_sourmash_taxonomy_to_metacoder to the differential heat tree viz (viz from the metacoder vignette)'

Visualization when we have a tree

When GTDB is the database, we have a tree we can use to build visualizations (although we would have to have a function to download it, and that might get annoying):
from: https://www.nature.com/articles/s41579-021-00562-3

[taylorreiter]

this heatmap is nicer than what I implemented over at Arcadia-Science/2022-prjna853785-sourmash.
https://www.biorxiv.org/content/10.1101/2022.08.17.504163v1.full.pdf

I also recently read a paper that kept all (species/genera/etc) that were present in at least one sample at 1% or above. I like the idea of doing that for this type of heatmap viz. by default it could be 1%, but it could be a user defined threshold

[taylorreiter]

same study as above, we could write a function that allows users to input specific (species, genomes, genera, etc) they want to viz and then make a heatmap of those

[taylorreiter]

ampvis2 also has pretty heatmaps

[taylorreiter]

Updates:

• The time series alluvial plot is finished
• The metacoder plot will work, but you need more than two groups at the moment, so i can't add it to the vignette with my current test data set.

[taylorreiter]

Code added for heat tree matrix in #46, but currently not evaluated as part of the vignette build. Waiting for metacoder to release a new version onto CRAN.