Read Xenium output

Read Xenium output

readXenium(
  data_dir,
  keep_type = "Gene Expression",
  feature_named_by = "Symbol",
  tiff_path = NULL,
  method_name = "10x"
)

Arguments

data_dir

a character specifying a single output directory as returned by Space Ranger, corresponding to one 10x Genomics Xenium sample.

keep_type

a character vector indicating the type of features to be included in the object. By default it is set to `"Gene Expression"`.

feature_named_by

a character indicating the way that the features are named. By default it is set to `"Symbol"`.

tiff_path

a character specifying the path of a tiff file output from BIDCell.

method_name

a character specifying the name of the method.

Value

A SpatialExperiment object

Examples

tenX_output_dir <- system.file("extdata/10x_output_subset", package = "CellSPA")
tenX_output_tif <- system.file("extdata/10x_output_subset/10x_from_csv_subset.tif",
                                package = "CellSPA")
spe_10x <- readXenium(tenX_output_dir,
                      tiff_path = tenX_output_tif)