Run spot-level quality control

Calculate common spot-level QC metrics for spatial transcriptomics data and label failed spots without running single-cell-specific checks such as doublet calling or ambient RNA decontamination.

Usage

RunSpotQC(
  srt,
  assay = NULL,
  return_filtered = FALSE,
  qc_metrics = c("outlier", "umi", "gene", "mito"),
  outlier_threshold = c("log10_nCount:lower:3", "log10_nFeature:lower:3",
    "spot_featurecount_dist:lower:3"),
  outlier_n = 1,
  UMI_threshold = 500,
  gene_threshold = 200,
  mito_threshold = 20,
  mito_pattern = c("MT-", "Mt-", "mt-"),
  mito_gene = NULL,
  verbose = TRUE,
  seed = 11
)

Arguments

srt

A Seurat object.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.

return_filtered

Logical indicating whether to return a spot-filtered Seurat object. Default is FALSE.

qc_metrics

QC metrics to apply. Available metrics are "outlier", "umi", "gene", and "mito".

outlier_threshold

Character vector specifying outlier thresholds as "metric:direction:nmads". Available default metrics are "log10_nCount", "log10_nFeature", and "spot_featurecount_dist".

outlier_n

Minimum number of outlier metrics required to fail a spot.

UMI_threshold

Minimum UMI count required to pass "umi" QC.

gene_threshold

Minimum detected gene count required to pass "gene" QC.

mito_threshold

Maximum mitochondrial percentage allowed by "mito" QC.

mito_pattern

Regex patterns used to identify mitochondrial genes.

mito_gene

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

verbose

Whether to print the message. Default is TRUE.

seed

Random seed for reproducibility.

Value

A Seurat object with spot QC metadata columns.

Examples

data(visium_human_pancreas_sub)
spatial <- RunSpotQC(
  visium_human_pancreas_sub,
  assay = "Spatial"
)
SpatialSpotPlot(spatial, group.by = "SpotQC")