Run SpotSweeper spatial quality control

Run SpotSweeper spatially aware spot-level quality control on a spatial Seurat object. The wrapper computes standard spot QC metrics, runs local outlier detection for each metric, optionally runs regional artifact detection per sample, and writes scop-style pass/fail metadata that can be visualized with SpatialSpotPlot().

Usage

RunSpotSweeper(
  srt,
  assay = NULL,
  layer = "counts",
  coord.cols = c("col", "row"),
  image = NULL,
  sample.by = NULL,
  metrics = NULL,
  directions = NULL,
  n_neighbors = 36,
  cutoff = 3,
  log = TRUE,
  run_artifact = TRUE,
  mito_pattern = c("MT-", "Mt-", "mt-"),
  mito_gene = NULL,
  mito_percent = NULL,
  mito_sum = NULL,
  n_order = 5,
  shape = c("hexagonal", "square"),
  prefix = "SpotSweeper",
  tool_name = "SpotSweeper",
  return_filtered = FALSE,
  store_results = TRUE,
  workers = 1,
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object.

assay

Assay used for expression. If NULL, the default assay is used.

layer

Assay layer used for expression values.

coord.cols

Metadata coordinate columns used when no Seurat image is available.

image

Name of the Seurat spatial image. If NULL, the first image is used when present.

sample.by

Optional metadata column identifying samples or images. If NULL, all spots are treated as one sample.

metrics

QC metrics used by SpotSweeper::localOutliers(). If NULL, nCount_<assay>, nFeature_<assay>, and percent.mito are used.

directions

Outlier direction for each metric. If NULL, count and feature metrics use "lower" and mitochondrial metrics use "higher".

n_neighbors

Number of nearest spatial neighbors for local outlier detection.

cutoff

Modified z-score cutoff passed to local outlier detection.

log

Whether SpotSweeper should log1p-transform local outlier metrics.

run_artifact

Whether to run SpotSweeper::findArtifacts() per sample.

mito_pattern

Regex prefixes used to identify mitochondrial genes.

mito_gene

Optional explicit mitochondrial gene vector. When provided, mito_pattern is ignored.

mito_percent

Metadata column used as mitochondrial percent for artifact detection. If NULL, percent.mito is used.

mito_sum

Metadata column used as mitochondrial counts for artifact detection. If NULL, mitochondrial counts are computed.

n_order, shape

Parameters passed to SpotSweeper::findArtifacts().

prefix

Prefix used for metadata columns.

tool_name

Name used to store detailed results in srt@tools.

return_filtered

Whether to return only spots passing SpotSweeper QC.

store_results

Whether to store detailed results in srt@tools.

workers

Number of workers passed to SpotSweeper local outlier detection.

verbose

Whether to print progress messages.

...

Additional named arguments passed to matching SpotSweeper backend functions when those arguments are supported by the installed version.

Value

A Seurat object with SpotSweeper QC metadata. When store_results = TRUE, detailed results are stored in srt@tools[[tool_name]].

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial$SpotSweeper_QC <- factor(
  ifelse(seq_len(ncol(spatial)) %% 9 == 0, "Fail", "Pass"),
  levels = c("Pass", "Fail")
)
spatial$SpotSweeper_nCount_Spatial_z <- as.numeric(scale(spatial$nCount_Spatial))

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

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


if (
  isTRUE(check_r("MicTott/SpotSweeper", verbose = FALSE)) &&
    requireNamespace("SpatialExperiment", quietly = TRUE)
) {
  spatial <- RunSpotSweeper(
    spatial,
    assay = "Spatial",
    coord.cols = c("x", "y"),
    n_neighbors = 12,
    run_artifact = FALSE,
    verbose = FALSE
  )

  SpatialSpotPlot(
    spatial,
    group.by = "SpotSweeper_QC",
    overlay_image = FALSE,
    coord.cols = c("x", "y")
  )
}
#> Error in check_r("MicTott/SpotSweeper", verbose = FALSE): could not find function "check_r"