make_processing_plots: Make default plot array associated with processing step.
In Chris-Cherry/sctools: Single cell analysis tools package

Creates a number of plots and csv files relating to cluster composition by all metadata in the ser object. This includes dim plots, feature plots, and pie plots for cluster composition. Point size is automatically scaled based on total number of cells and 10 feature plots. Reductions used are umap and phate.

make_processing_plots(
  ser,
  out_dir = "1_process/",
  colors = NULL,
  use_phate = TRUE,
  cluster_enrichment_pvals = FALSE
)

`ser`	Seurat object to process.
`out_dir`	Output directory
`colors`	Optional color schemes for metadata. Each scheme (for a given metadata) must be a vector of colors named with the levels of the metadata. The colors object is a named list of these named vectors. The name of the scheme must match the metadata name in the seurat object.
`use_phate`	Boolean indicating whether to use phate dimensional reduction for plots.
`cluster_enrichment_pvals`	Boolean indicating whether to calculate P values for clusters by metadata.