FEAT: Lineage & UpSet plots

[jananiravi]

Lineage plots

• [x] 100% plots: we should make sure they are readable. If not, the plot should be scrollable to ensure minimal text overlap.
• [ ] genomic Context network, lineage plots | unreadable
• [ ] reduce the number of lineages | combine into larger groups having multiple phyla
• [x] what to do with viruses?
• [x] remove '*' characters from plotting
• [x] change bacteria, archaea, and eukaryota to B, A, and E
• [x] for all, add domains vs lineages
• [x] for all, add DA/GCs vs lineages
• [x] add alternate color schemes (dropdown?)
• [ ] plot cleanup with
  • [ ] ggsci color schemes
  • [ ] ggpubr
  • [ ] tidytext (less applicable; ggrepel)
  • [x] sunburstr
  • [ ] gganimate
  • [ ] cowplot
  • [ ] other: ggplot extension gallery
• [ ] Option to normalize heatmap by %species within a lineage

UpSet plots

• [ ] upset plot: possible to limit by the number of rows/columns?
• [x] upset plot: ones without the dots -- eliminate?
• [ ] upset + lineage stacked plot
• [ ] complexupset
• [ ] cleanup complex upset!
• [ ] add alternate color schemes (dropdown?)

[jakekrol]

@jananiravi for these UpSet checklist items. Could you link to examples/packages, where possible, for a starting point? Thanks

[jakekrol]

Can we add which analysis/plot each package (gganimate, cowplot, etc.) corresponds to?