Viz notes

[sckott]

• add phylopic sil's - see #3
• facet by taxonomic rank? e.g.,

# facet by rank
x %>% <other ggplot2 code> %>% facet_rank(phylum)
# custom name vs. name OR rank vs. rank
x %>% <other ggplot2 code> %>% compare_ranks(phylum)
x %>% <other ggplot2 code> %>% compare_names(Helianthus, Quercus)

with each facet being a diff. phylum

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any other ideas for taxonomically based vizualizations ? @cboettig @zachary-foster

p.s.. Zach, we can already leverage viz tools you have in metacoder I think or just point people to metacoder?

[zachary-foster]

Hi Scott, is this package an extension to ggplot2? I dont remember seeing it before.

any other ideas for taxonomically based vizualizations ?

Anything meant for hierarchal data has some potential. Here are a few:

• treemaps: https://github.com/mtennekes/treemap
• sunbursts: https://github.com/timelyportfolio/sunburstR

Zach, we can already leverage viz tools you have in metacoder I think or just point people to metacoder?

the metacoder heat_tree function returns uses ggplot2, so probably. I am planning on rewriting it soon, so if there is any functionality that would be helpful, feel free to open an issue to request it. A benefit of using metacoder is that taxa is already used there as inputs.

Btw, I have plans to add phylopic images to metacoder trees as well

[sckott]

no, not a ggplot2 extension, just part of it will be viz. not sure where this is going yet, just exploring

thanks! @zachary-foster i'll check these out

[cboettig]

Adding to the random notes: some nice tree visualizations in ggraph as well, includes treemaps and particularly the dendrogram layouts. https://cran.r-project.org/web/packages/ggraph/vignettes/Layouts.html Currently these don't include branch lengths, but could be a nice visualization for the rank-based trees we get from stuff like ncbi and itis. @thomasp85 has done a really nice job in making these plots work pretty well with very large graphs; both in performance terms and in creating a readable / pleasing visual. Might be very cool to combine with phylopic silhouettes....

[thomasp85]

Fwiw branch length will get supported in the next development cycle

[sckott]

thanks @cboettig and @thomasp85

note to self to check out: https://cran.rstudio.com/web/packages/data.tree/