Check input spe

Source: R/check_spe.R

This function checks that the spe object has the appropriate structure. For more details please check the vignette documentation.

check_spe(
  spe,
  variables = c("sum_umi", "sum_gene", "expr_chrM", "expr_chrM_ratio"),
  datatype = c("Visium", "Xenium")
)

Arguments

spe

A SpatialExperiment-class object. See fetch_data() for how to download some example objects or read10xVisiumWrapper() to read in spaceranger --count output files and build your own spe object.

variables

A character() vector of variable names expected to be present in colData(spe).

datatype

A character(1) specifying the type of spatial transcriptomics data stored in spe. Supported options are:

"Visium"

(Default) Expects pxl_col_in_fullres and pxl_row_in_fullres as columns of spatialCoords(spe). Enables image handling via the spatialData slot.

"Xenium"

Expects x_centroid and y_centroid as columns of spatialCoords(spe).

Value

The input object if all checks are passed.

See also

Other Check input functions: check_modeling_results(), check_sce(), check_sce_layer()

Author

Brenda Pardo, Leonardo Collado-Torres

Examples


if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("spe")) spe <- fetch_data("spe")

    ## Check the object
    check_spe(spe)
}
#> 2026-09-28 14:53:10.666643 loading file /github/home/.cache/R/BiocFileCache/e2d3506994e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> class: SpatialExperiment 
#> dim: 33538 47681 
#> metadata(0):
#> assays(2): counts logcounts
#> rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
#>   ENSG00000268674
#> rowData names(9): source type ... gene_search is_top_hvg
#> colnames(47681): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#>   TTGTTTCCATACAACT-1 TTGTTTGTGTAAATTC-1
#> colData names(69): sample_id Cluster ... array_row array_col
#> reducedDimNames(6): PCA TSNE_perplexity50 ... TSNE_perplexity80
#>   UMAP_neighbors15
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor