Run SpatialQM quality metrics

Run selected SpatialQM quality-control metrics on a spatial Seurat object and store a compact, scop-style result bundle in srt@tools. SpatialQM currently expects a RNA assay for object-first metrics, so this wrapper maps the selected assay layer to a temporary RNA assay without modifying the returned object. SpatialQM is an optional GitHub dependency installable with remotes::install_github("Center-for-Spatial-OMICs/SpatialQM").

Usage

RunSpatialQM(
  srt,
  assay = NULL,
  layer = "counts",
  metrics = c("n_cells", "tx_per_cell", "max_detection"),
  features = NULL,
  sample_id = NULL,
  platform = NULL,
  tool_name = "SpatialQM",
  store_results = TRUE,
  on_error = c("error", "warning"),
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object.

assay

Assay used for SpatialQM input. If NULL, the default assay is used.

layer

Assay layer used as counts for SpatialQM.

metrics

SpatialQM metrics to run. Supported aliases include "n_cells", "tx_per_cell", "tx_per_area", "tx_per_nuc", "mean_expression", "mean_signal_ratio", "cell_tx_fraction", "max_ratio", "max_detection", "mecr", "morans", "silhouette", "sparsity", and "entropy". The defaults are the object-first metrics supported by the current upstream API without raw transcript or control-probe inputs; other metrics remain explicitly selectable.

features

Optional feature vector passed to metrics that support a features argument.

sample_id, platform

Optional values used to populate missing sample_id and platform metadata columns expected by some SpatialQM metrics.

tool_name

Name used to store results in srt@tools.

store_results

Whether to store results in srt@tools.

on_error

Whether a failed metric should stop the wrapper ("error") or be recorded in the result bundle with a warning ("warning").

verbose

Whether to print the message. Default is TRUE.

...

Additional named arguments passed to SpatialQM metric functions when the installed function exposes matching formal arguments.

Value

A Seurat object. When store_results = TRUE, results are stored in srt@tools[[tool_name]].

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub

spatial <- RunSpatialQM(
  spatial,
  assay = "Spatial",
  layer = "counts",
  metrics = "n_cells",
  platform = "Visium",
  verbose = FALSE
)
#> Error in RunSpatialQM(spatial, assay = "Spatial", layer = "counts", metrics = "n_cells",     platform = "Visium", verbose = FALSE): SpatialQM metric "n_cells" failed: there is no package called
#> ‘SpatialQM’
spatial@tools$SpatialQM$summary
#> NULL