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Simulated VisiumHD 16 µm binned SpatialExperiment dataset

Source: R/data.R
visiumHD_16um_simulated_spe.Rd

A simulated SpatialExperiment object mimicking a 10x Genomics Visium spatial transcriptomics layout. The dataset contains spot-level spatial coordinates and cluster annotations, and is intended for testing.

Usage

data(visiumHD_16um_simulated_spe)

Format

A SpatialExperiment object with:

assays

One dummy assay (required container structure)

colData

Spot metadata including barcode and cluster

spatialCoords

Numeric matrix of x/y spot coordinates

Source

Simulated internally for package development.

Details

This dataset contain only gene expression values for one gene named FAKE_GENE. The dummy assay is included solely to satisfy the SummarizedExperiment container requirements.

Spot coordinates follow a Visium-like squared grid. Cluster labels are simulated and have no biological meaning.

The layout is intended to mimic a Visium HD *binned* layer (e.g., 16 µm bin size), where each spot represents one bin arranged on an adjacent square grid.

See also

"visiumHD_16um_simulated_spe"

Examples

data(visiumHD_16um_simulated_spe)

visiumHD_16um_simulated_spe
#> class: SpatialExperiment 
#> dim: 1 1000 
#> metadata(0):
#> assays(1): counts
#> rownames(1): FAKE_GENE
#> rowData names(0):
#> colnames(1000): bin16_1 bin16_41 ... bin16_960 bin16_1000
#> colData names(3): barcode_id cluster sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(0):