Release Prep v2.2.0

[samuel-marsh]

To Do:

• [x] anndata warnings (https://github.com/samuel-marsh/scCustomize/issues/162)
• [x] LIGER 2.0 compatibility or warning messages (https://github.com/samuel-marsh/scCustomize/issues/161)
• [x] Spatial Plots (if time) (https://github.com/samuel-marsh/scCustomize/issues/160)
• [x] ~ggprism workaround if not fixed before CRAN removal (https://github.com/csdaw/ggprism/pull/25)~
• [x] Metrics Single Directory
• [x] Factor_Cor_Plot
• [x] Add_Hemo
• [ ] Update Vignettes
• [ ] Update pkgdown site

[samuel-marsh]

~- [ ] Add Spatial Assay to as.anndata?~ Not now. Have to figure out some image conversion metrics and not priority for time being.

[samuel-marsh]

Final LIGER related changes:

• [x] Idents()
• [x] Rename_Clusters()
• [ ] Factor Cor Plot Clustering

[samuel-marsh]

Vignette Changes Needed:

• [x] seq_zeros
• [x] Chicken as species
• [ ] Spatial Plots
• [x] cutoff line width
• [x] Add mito ribo dual
• [x] scripts for qc lists

LIGER Vignettes:

• [ ] Subset liger
• [ ] liger cells by identities
• [ ] LIGER/Seurat Shared Generics
• [ ] Rename Clusters for LIGER
• [ ] Factor Cor Plots