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Run semla local G spatial autocorrelation

Source: R/RunSemla.R
RunSemlaLocalG.Rd

Use semla::RunLocalG() on a Staffli-enabled Seurat object. Results are written by semla to metadata or to an assay, depending on store_in_metadata. SCOP provides no dedicated plot for this result; retrieve its schema record with GetSpatialResult() and inspect the recorded output columns or assay.

Usage

RunSemlaLocalG(
  srt,
  features,
  alternative = NULL,
  store_in_metadata = TRUE,
  assay_name = "GiScores",
  image_type = "tissue_lowres",
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object with spatial image data.

features

Features passed to semla::RunLocalG().

alternative

Alternative hypothesis passed to semla. Use NULL to keep semla's default behavior.

store_in_metadata

Whether semla should store results in metadata.

assay_name

Assay name used by semla when store_in_metadata = FALSE.

image_type

Image scale used by semla::UpdateSeuratForSemla() when the object does not already contain a Staffli object.

verbose

Whether to print the message. Default is TRUE.

...

Additional arguments passed to semla.

Value

A Seurat object.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)
features <- rownames(spatial)[1:3]
spatial[[paste0(features[1], "_localG")]] <- as.numeric(scale(spatial$x))

SpatialSpotPlot(
  spatial,
  group.by = paste0(features[1], "_localG"),
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)


spatial <- RunSemlaLocalG(
  spatial,
  features = features,
  store_in_metadata = TRUE,
  verbose = FALSE
)
#> ℹ Found VisiumV2 object(s).
#> 
#> ── Collecting data from @images slot 
#> ! Array coordinates are not available for non-VisiumHD datasets. Please consider using semla's own functions to load the data. See '?ReadVisiumData()'