Skip to contents

Run official SpaTalk spatial communication analysis

Source: R/RunSpaTalk.R
RunSpaTalk.Rd

Run the official SpaTalk R backend for single-cell spatial data or spot data with a single-cell reference. Results are stored as a compact method bundle and added to SCOP's unified CCC table.

Usage

RunSpaTalk(
  srt,
  group.by,
  mode = c("auto", "single_cell", "spot"),
  reference = NULL,
  reference.group.by = NULL,
  species = c("Human", "Mouse"),
  assay = NULL,
  layer = "counts",
  reference.assay = NULL,
  reference.layer = "counts",
  image = NULL,
  coord.cols = c("col", "row"),
  deconvolution = c("NNLM", "RCTD", "none"),
  rctd.tool = "RCTD",
  result.name = "default",
  store.object = c("minimal", "full"),
  overwrite = FALSE,
  backend = c("cpp", "r"),
  verbose = TRUE,
  ...
)

Arguments

srt

A `Seurat` spatial object.

group.by

Metadata column containing cell labels for single-cell mode.

mode

Analysis mode. `"auto"` selects spot mode when `reference` is supplied and single-cell mode otherwise.

reference

Optional single-cell `Seurat` reference for spot mode.

reference.group.by

Cell-type column in `reference`.

species

SpaTalk species database.

assay, layer

Spatial assay and raw-count layer.

reference.assay, reference.layer

Reference assay and raw-count layer.

image

Explicit spatial image. Required for multi-image objects.

coord.cols

Metadata coordinate columns used when no image is present.

deconvolution

Spot deconvolution mode. `"NNLM"` runs SpaTalk method 1; `"RCTD"` reuses `srt@tools[[rctd.tool]]$weights` from [RunRCTD()] (or an explicitly supplied `dec_result`); `"none"` requires a named external `dec_result` matrix in `...`. Imported matrices use SpaTalk method 2.

rctd.tool

Tool key containing stored RCTD weights when `deconvolution = "RCTD"`.

result.name

Stored result name.

store.object

Whether to store the full upstream SpaTalk object.

overwrite

Whether to replace an existing named result.

backend

Backend used only for SCOP CCC result aggregation.

verbose

Whether to print progress messages.

...

Named arguments forwarded to compatible official SpaTalk steps.

Value

The input `Seurat` object with `srt@tools$SpaTalk` and unified CCC results updated.

References

<https://github.com/ZJUFanLab/SpaTalk>

Examples

if (FALSE) { # \dontrun{
available <- unname(unlist(thisutils::check_r(
  c("linxihui/NNLM", "ZJUFanLab/SpaTalk"), verbose = FALSE
)))
if (length(available) == 2L && all(available)) {
  spatial <- RunSpaTalk(
    spatial,
    group.by = "celltype",
    mode = "single_cell",
    image = "slice1"
  )
}
} # }