Initiate an object of class SPATA2 from platform Xenium

This function initiates a SPATA2 object with data generated using the 10x Genomics Xenium platform.

initiateSpataObjectXenium(sample_name, directory_xenium, verbose = TRUE)

Arguments

sample_name

Character value. The name with which to identify the SPATA2 object.

directory_xenium

Character value. Directory to a Xenium output folder.

verbose

Logical. If TRUE, informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

Value

A SPATA2 object from the Xenium platform. Default for pt_size is set to 0.1 which might need adjustment.

Details

The function requires a directory containing the output files from a 10x Genomics Xenium experiment specified with the argument directory_xenium. This directory (below denoted as ~) must include the following sub-directories:

  • ~/cell_feature_matrix: A folder that contains the following files:

    • ~/cell_feature_matrix/barcodes.tsv.gz: The cell barcodes.

    • ~/cell_feature_matrix/features.tsv.gz: The feature (gene) names.

    • ~/cell_feature_matrix/matrix.mtx.gz: The raw count data matrix.

  • ~/cells.csv.gz: The cellular positions.

Xenium works in micron space. The coordinates of the cellular centroids are provided in unit um. Therefore no pixel scale factor must be computed or set to work with SI units.

See also

setDefault()