Load a previously saved AlertSystem state into a Seurat object

This helper reads an AlertSystem RDS file (created by AlertSystemScore(..., out_dir = ...) or SaveAlertSystem()) and attaches it to seurat_obj@misc[[misc_name]].

Usage

LoadAlertSystem(
  seurat_obj,
  file,
  misc_name = "AlertSystem",
  overwrite = TRUE,
  verbose = TRUE
)

Arguments

seurat_obj: A Seurat object.
file: Path to an RDS file containing an AlertSystem list (e.g. "AlertSystem_M6_M6_up_AlertSystem_info.rds").
misc_name: Name of the misc slot where the state should be stored. Default: "AlertSystem".
overwrite: Logical; if FALSE and a state already exists at misc_name, an error is thrown. Default: TRUE.
verbose: Logical; print a short message upon successful load.

Value

The updated Seurat object.

Details

Typically, this RDS file will be the *_AlertSystem_info.rds file written by AlertSystemScore, which contains per_cell, metrics, and params in a single list. Any associated metrics CSV (e.g. *_metrics.csv) is not required for loading and plotting, but can be inspected separately.

Note: this does not modify seurat_obj@meta.data; per-cell scores remain accessible via seurat_obj@misc[[misc_name]]$per_cell.

Examples

if (FALSE) { # \dontrun{
test_obj <- LoadAlertSystem(
  seurat_obj = test_obj,
  file       = "PathToAlertSystemResults/AlertSystem_XXXXXX_AlertSystem_info.rds"
)
} # }