Run CytoSPACE spatial assignment

Run CytoSPACE spatial assignment

Usage

RunCytoSPACE(
  srt,
  reference,
  reference_label,
  assay = NULL,
  reference_assay = NULL,
  layer = "counts",
  reference_layer = "counts",
  features = NULL,
  cell_fractions = NULL,
  n_cells_per_spot = NULL,
  mean_cell_numbers = 5,
  scRNA_max_transcripts_per_cell = 1500,
  sampling_method = "duplicates",
  seed = 1,
  prefix = "CytoSPACE",
  store_results = TRUE,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

reference

Reference Seurat object containing annotated single cells.

reference_label

Metadata column in reference with cell type labels.

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.

reference_assay

Assay used in reference.

layer, reference_layer

Assay layers used for spatial and reference expression.

features

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

cell_fractions

Optional cell-type fractions. Provide a named numeric vector, one-row matrix/data.frame, or a spot-by-cell-type matrix/data.frame. Spot-level rows are aggregated to the global composition used by the default CytoSPACE assignment workflow.

n_cells_per_spot

Optional number of cells assigned to each spatial spot. If NULL, counts are estimated from spatial RNA reads with mean_cell_numbers.

mean_cell_numbers

Mean number of cells per spot. Default 5, matching the CytoSPACE Visium default.

scRNA_max_transcripts_per_cell

Maximum reference transcripts per cell before assignment. Default 1500, matching CytoSPACE.

sampling_method

Sampling method. Only "duplicates" is supported in the package runtime.

seed

Random seed used for deterministic reference downsampling and duplicate sampling.

prefix

Prefix for metadata columns.

store_results

Whether to store detailed assignment results in srt@tools.

verbose

Whether to print the message. Default is TRUE.

Value

A Seurat object with CytoSPACE metadata columns and detailed results stored in srt@tools[["CytoSPACE"]].

Examples

data(visium_human_pancreas_sub)
data(pancreas_sub)
features_use <- intersect(
  rownames(visium_human_pancreas_sub),
  rownames(pancreas_sub)
)
spatial <- RunCytoSPACE(
  visium_human_pancreas_sub,
  reference = pancreas_sub,
  reference_label = "CellType",
  features = features_use,
  mean_cell_numbers = 1
)
#> ℹ [2026-07-02 09:31:33] Estimated CytoSPACE cell type fractions for 5 reference labels
#> ℹ [2026-07-02 09:31:33] Run CytoSPACE with 4 features, 686 sampled reference cells, and 1986 spatial spots
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#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:33] Assign sampled reference cells to spatial spots  ■■■■■■…
#> ℹ [2026-07-02 09:31:41] Build CytoSPACE assignment summaries
#> ℹ [2026-07-02 09:31:41] CytoSPACE assignments stored in `srt@tools[['CytoSPACE']]` and metadata prefix "CytoSPACE"

SpatialSpotPlot(
  visium_human_pancreas_sub,
  group.by = "coda_label",
  theme_use = "theme_scop"
)


SpatialSpotPlot(
  spatial,
  group.by = "CytoSPACE_dominant_type",
  theme_use = "theme_scop"
)