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Run CARD spatial deconvolution

Source: R/RunCARD.R
RunCARD.Rd

Estimate spot-level cell-type proportions from spatial expression and an annotated single-cell reference using CARD or CARDspa.

Usage

RunCARD(
  object,
  reference,
  reference_label,
  assay = NULL,
  reference_assay = NULL,
  layer = "counts",
  reference_layer = "counts",
  features = NULL,
  image = NULL,
  coord.cols = c("col", "row"),
  sample_varname = NULL,
  minCountGene = 100,
  minCountSpot = 5,
  ct_select = NULL,
  prefix = "CARD",
  tool_name = "CARD",
  store_results = TRUE,
  round_counts = TRUE,
  create_card_params = list(),
  card_deconvolution_params = list(),
  verbose = TRUE,
  ...,
  coordinate_space = c("raw", "legacy_display"),
  srt = NULL
)

Arguments

object

Spatial Seurat object used as the RCTD query.

reference

Reference Seurat object containing annotated single cells.

reference_label

Metadata column in reference with cell type labels.

assay

Assay used in object. If NULL, the default assay is used.

reference_assay

Assay used in reference. Only cells present in this assay are used, with reference labels aligned by cell ID.

layer, reference_layer

Assay layers used for spatial and reference raw counts.

features

Features used for CARD. If NULL, shared features are used.

image

Name of the Seurat spatial image used to recover coordinates when coord.cols are not available.

coord.cols

Metadata coordinate columns used when no image coordinate source is requested or available.

sample_varname

Optional metadata column in reference containing sample labels. When NULL, all reference cells are assigned to one sample.

minCountGene, minCountSpot

Filtering parameters passed to CARD::createCARDObject() or CARDspa::createCARDObject() when supported.

ct_select

Optional cell types to keep in CARD.

prefix

Prefix for metadata columns.

tool_name

Name used to store detailed results in srt@tools.

store_results

Whether to store detailed RCTD results in srt@tools.

round_counts

Whether to round non-integer values before passing data to spacexr. RCTD requires integer count matrices; rounding is a compatibility option and does not recover original counts.

create_card_params

Additional parameters passed to createCARDObject().

card_deconvolution_params

Additional parameters passed to CARD_deconvolution().

verbose

Whether to print the message. Default is TRUE.

...

Additional parameters passed to the RCTD run step.

coordinate_space

Coordinate space used for distance-sensitive input. The default is raw acquisition coordinates, so backend distances use raw coordinate units. Use "legacy_display" explicitly to reproduce the display-scaled coordinates used before scop 0.9.0.

srt

Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A Seurat object with CARD proportion columns in metadata and dominant cell type summaries. When store_results = TRUE, detailed results are stored in srt@tools[[tool_name]].

Examples

if (FALSE) { # \dontrun{
data(visium_human_pancreas_sub)
data(panc8_sub)
keep_spots <- unique(round(seq(
  1,
  ncol(visium_human_pancreas_sub),
  length.out = 120
)))
spatial <- visium_human_pancreas_sub[, keep_spots]
# Results are conditional on the three reference cell types used here.
reference <- panc8_sub[, panc8_sub@meta.data[["celltype"]] %in%
  c("ductal", "alpha", "beta")]
features_use <- head(intersect(rownames(spatial), rownames(reference)), 300)
spatial <- RunCARD(
  object = spatial,
  reference = reference,
  reference_label = "celltype",
  assay = "Spatial",
  reference_assay = "RNA",
  layer = "counts",
  reference_layer = "counts",
  features = features_use,
  coord.cols = c("x", "y"),
  verbose = FALSE
)
SpatialDeconvolutionPlot(
  spatial,
  tool_name = "CARD",
  plot_type = "dominant",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)
} # }