Run STdeconvolve reference-free spatial deconvolution

Infer expression topics and their spot-level proportions using STdeconvolve.

Usage

RunSTdeconvolve(
  object,
  assay = NULL,
  layer = "counts",
  features = NULL,
  k = NULL,
  k_candidates = 2:9,
  opt = "min",
  clean_counts = TRUE,
  clean_counts_params = list(),
  restrict_corpus = TRUE,
  restrict_corpus_params = list(),
  fit_lda_params = list(),
  get_beta_theta_params = list(),
  prefix = "STdeconvolve",
  tool_name = "STdeconvolve",
  store_results = TRUE,
  round_counts = TRUE,
  verbose = TRUE,
  ...,
  srt = NULL
)

Arguments

object: A Seurat object containing spatial expression data.
assay: Assay used as STdeconvolve input. If NULL, the default assay is used.
layer: Assay layer used as STdeconvolve input.
features: Features passed to the topic model. If NULL, all features in the selected assay are used.
k: Number of topics. If NULL, models are fit over k_candidates and STdeconvolve::optimalModel() is used to choose a model.
k_candidates: Candidate topic numbers used when k = NULL.
opt: Optimal model selector passed to STdeconvolve::optimalModel().
clean_counts: Whether to call STdeconvolve::cleanCounts().
clean_counts_params: Additional parameters passed to STdeconvolve::cleanCounts().
restrict_corpus: Whether to call STdeconvolve::restrictCorpus().
restrict_corpus_params: Additional parameters passed to STdeconvolve::restrictCorpus().
fit_lda_params: Additional parameters passed to STdeconvolve::fitLDA().
get_beta_theta_params: Additional parameters passed to STdeconvolve::getBetaTheta().
prefix: Prefix for topic proportion metadata columns.
tool_name: Name used to store detailed results in srt@tools.
store_results: Whether to store detailed topic matrices in srt@tools.
round_counts: Whether to round non-integer counts before model fitting. This is a preprocessing choice and does not recover original counts.
verbose: Whether to print messages.
...: Additional arguments passed to the STdeconvolve fit steps.
srt: Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A Seurat object with topic proportions in metadata and detailed results stored in srt@tools[[tool_name]] when store_results = TRUE.

Examples

if (FALSE) { # \dontrun{
data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
counts <- GetAssayData5(spatial, assay = "Spatial", layer = "counts")
features <- names(sort(Matrix::rowSums(counts), decreasing = TRUE))[
  seq_len(min(300L, nrow(counts)))
]
spatial <- RunSTdeconvolve(
  spatial,
  assay = "Spatial",
  layer = "counts",
  features = features,
  k = 3,
  verbose = FALSE
)
STdeconvolvePlot(
  spatial,
  topics = 1L,
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)
} # }