scAdvanced updates: dir_create and plotting

[sjspielman]

Closes #692
Closes #734

This PR updates scAdvanced notebooks by:

• using fs::dir_create instead of dir.create
• all colour -> color, and use brewer dark2 where we can
  • I used the rendered notebooks as they appeared in march 2023 to determine which plots to use dark2 with:
    • refresher notebook
    • integration
    • differential expression
• in the integration notebook, I also made the ggplot calls a bit more consistent with a more similar line order

[jashapiro]

LGTM