[FEAT] Plotting lineage & domain architectures

[jananiravi]

Lineage plots

• 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
• what to do with viruses?
• remove '*' characters from plotting
• change bacteria, archaea, and eukaryota to B, A, and E
• for all, add domains vs lineages
• for all, add DA/GCs vs lineages
• add alternate color schemes (dropdown?)
• plot cleanup with
  • ggsci color schemes
  • ggpubr
  • tidytext (less applicable; ggrepel)
  • 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?
• 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?