Run STdeconvolve reference-free spatial deconvolution

Estimate spot-level topic proportions from a spatial Seurat object using the optional STdeconvolve package.

Usage

RunSTdeconvolve(
  srt,
  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,
  ...
)

Arguments

srt: Spatial Seurat object used as the RCTD query.
assay: Assay used in srt. If NULL, the default assay is used.
layer: Assay layer used as STdeconvolve input.
features: Features used for RCTD. If NULL, shared features 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 metadata columns.
tool_name: Name used to store detailed results in srt@tools.
store_results: Whether to store detailed RCTD results in srt@tools.
round_counts: Whether to round non-integer counts before model fitting.
verbose: Whether to print the message. Default is TRUE.
...: Additional parameters passed to the RCTD run step.

Value

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

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
topic_weights <- data.frame(
  STdeconvolve_prop_topic_1 = seq(0.75, 0.20, length.out = ncol(spatial)),
  STdeconvolve_prop_topic_2 = seq(0.20, 0.70, length.out = ncol(spatial)),
  STdeconvolve_prop_topic_3 = 0.10,
  row.names = colnames(spatial)
)
topic_weights <- topic_weights / rowSums(topic_weights)
spatial <- Seurat::AddMetaData(spatial, topic_weights)
spatial$STdeconvolve_dominant_type <- sub(
  "^STdeconvolve_prop_",
  "",
  colnames(topic_weights)[max.col(topic_weights)]
)
spatial$STdeconvolve_max_prop <- apply(topic_weights, 1, max)

SpatialSpotPlot(
  spatial,
  group.by = "STdeconvolve_dominant_type",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)

STdeconvolvePlot(
  spatial,
  topics = 1:2,
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)

if (requireNamespace("scatterpie", quietly = TRUE)) {
  STdeconvolvePlot(
    spatial,
    plot_type = "pie",
    overlay_image = FALSE,
    coord.cols = c("x", "y")
  )
}


if (
  isTRUE(check_r("JEFworks-Lab/STdeconvolve", verbose = FALSE))
) {
spatial <- RunSTdeconvolve(
  spatial,
  assay = "Spatial",
  features = rownames(spatial)[1:300],
  k = 3,
  verbose = FALSE
)
}
#> Error in check_r("JEFworks-Lab/STdeconvolve", verbose = FALSE): could not find function "check_r"