SPOTlight deconvolution of spatial data using an `screference`

Usage

spotlight_deconvolute(
  spatial_obj,
  scref,
  model = "ns",
  n_top = NULL,
  min_prop = 0,
  cache_path = NULL
)

spatial_obj: an `Seurat` object with a Spatial assay
scref: an object of `screference`
model: character string indicating which model to use when running NMF. Either "ns" (default) or "std".
n_top: integer scalar specifying the number of markers to select per group. By default NULL uses all the marker genes to initialize the model.
min_prop: scalar in [0,1] setting the minimum contribution expected from a cell type in x to observations in y. By default 0.
cache_path: a path to cache the results

a tibble with deconvolution fractions