Unified deconvolution orchestration and method runners

run_deconvolution() dispatches requested methods using the AEGIS method registry, standardizes outputs to the shared AEGIS deconvolution contract, and returns results ready for as_aegis() / run_aegis().

run_aegis_full() combines one-shot deconvolution dispatch with the existing AEGIS downstream pipeline.

Method-specific runner wrappers are included for directly runnable R-native methods and optional Python-backed methods.

Usage

run_deconvolution(
  seu,
  reference,
  methods = c("SPOTlight", "RCTD", "CARD"),
  sample_id = NULL,
  normalize = TRUE,
  strict = TRUE,
  use_python = TRUE,
  runner_overrides = NULL,
  runner_args = NULL,
  ...
)

run_aegis_full(
  seu,
  reference,
  methods = c("SPOTlight", "RCTD", "CARD"),
  markers = NULL,
  strict = TRUE,
  use_python = TRUE,
  normalize = TRUE,
  ...
)

run_spotlight(seu, reference, normalize = TRUE, strict = TRUE, ...)

run_card(seu, reference, normalize = TRUE, strict = TRUE, ...)

run_rctd(seu, reference, normalize = TRUE, strict = TRUE, ...)

run_cell2location(seu, reference, normalize = TRUE, strict = TRUE, ...)

run_destvi(seu, reference, normalize = TRUE, strict = TRUE, ...)

run_tangram(seu, reference, normalize = TRUE, strict = TRUE, ...)

run_stereoscope(seu, reference, normalize = TRUE, strict = TRUE, ...)

Arguments

seu: A Seurat spatial object.
reference: Reference input used by runnable methods.
methods: Character vector of method names.
sample_id: Optional sample identifier recorded in deconvolution output metadata.
normalize: Logical; row-normalize outputs to proportions when possible.
strict: Logical; strict error behavior for unsupported/missing dependencies or failed execution.
use_python: Logical; allow Python-backed methods via reticulate.
runner_overrides: Optional named list of runner functions keyed by method, mainly for advanced usage/testing.
runner_args: Optional named list of per-method argument lists passed to the selected runner.
markers: Optional marker list used by run_aegis_full().
...: Additional arguments forwarded to method runners.

Value

run_deconvolution() returns a list with:
seu, deconv, methods_run, methods_skipped, and messages.
run_aegis_full() returns an aegis object.
Method-specific runners return spot-by-celltype numeric matrices.