vignettes updates

[patrickjdanaher]

The vignette should be more detailed and up-to-date.

Goal: support full use of package.

Different vignettes for different use cases?

1. Supervised, including rescaling for platform effects.
2. Unsupervised
3. Semi-supervised with ioprofiles, including full anchor selection workflow
4. Defining cohorts?
5. refineClusters? Show umap/flightpath of a couple clustering solutions, and show the refineClusters calls you'd make.

[patrickjdanaher]

Supervised vignette:

• data: 1 FOV of SCH
• show how to access reference profile - describe how to access on github, but just have the profiles in the package data
• update reference profile
• cohorting based on IF
• insitutypeML
• flightpath
• refineClusters: show merging, sub-clustering, and deleting

Unsupervised vignette:

• data: mini_nsclc
• cohorting based on IF
• insitutypeML
• flightpath
• refineClusters: show merging, sub-clustering, and deleting