Refine figure aesthetics

[huddlej]

Description

Refines figure aesthetics to improve interpretation of phylogenies and identification of clades in both phylogenies and embeddings.

Development checklist

• [x] Early H3N2 HA plots
  • [x] Add Nextstrain clade labels to tree and embeddings
  • [x] Plot trees without variable branch widths
  • [x] Plot trees with rectangular layout
• [x] Late H3N2 HA plots
  • [x] Add Nextstrain clade labels to tree and embeddings
  • [x] Plot trees without variable branch widths
  • [x] Plot trees with rectangular layout
• [x] HA/NA plots
  • [x] Add TreeKnit MCC labels to tree and embeddings
  • [x] Plot trees without variable branch widths
  • [x] Plot trees with rectangular layout
  • [x] Assign better colors
  • [x] Reference MCCs 5 and 10 in manuscript as another phylogenetically adjacent pair
• [x] Early SC2 plots
  • [x] Add Nextstrain clade labels to tree and embeddings
  • [x] Plot trees without variable branch widths
  • [x] Plot trees with rectangular layout
• [x] Late SC2 plots
  • [x] Add missing figures for tree and embeddings colored Nextstrain clade
  • [x] Add Nextstrain clade labels to tree and embeddings
  • [x] Plot trees without variable branch widths
  • [x] Plot trees with rectangular layout

Related issues

Closes #100 Closes #105 Closes #106