Package 'XeniumIO'

XeniumIO: Import and represent Xenium data from the 10X Xenium Analyzer

Description

The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include 'parquet', 'h5', and 'mtx' files. The package mainly represents data as SpatialExperiment objects.

Author(s)

Maintainer: Marcel Ramos [email protected] (ORCID)

Other contributors:

• Dario Righelli [contributor]

• Estella Dong [contributor]

See Also

Useful links:

• https://github.com/waldronlab/XeniumIO

• Report bugs at https://github.com/waldronlab/XeniumIO/issues

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A class to represent Xenium output data

Description

This class is a composed class of TENxFileList which can contain a list of TENxFile objects for the cell-feature matrix. It is meant to handle a single Xenium sample from 10X Genomics.

Usage

TENxXenium(
  resources,
  xeniumOut,
  sample_id = "sample01",
  format = c("mtx", "h5"),
  boundaries_format = c("parquet", "csv.gz"),
  spatialCoordsNames = c("x_centroid", "y_centroid"),
  ...
)

## S4 method for signature 'TENxXenium,ANY,ANY'
import(con, format, text, ...)

Arguments

resources	A TENxFileList object or a file path to the tarball containing the matrix / assay data resources.
xeniumOut	character(1) The path to the Xenium output directory.
sample_id	character(1) A single string specifying the sample ID.
format	The format of the output. If missing and con is a file name, the format is derived from the file extension. This argument is unnecessary when con is a derivative of BiocFile.
boundaries_format	character(1) Either "parquet" or "csv.gz" to specify the file extension of the boundaries file. Default is "parquet".
spatialCoordsNames	character() A vector of strings specifying the names of the columns in the spatial data containing the spatial coordinates.
...	In the constructor, additional arguments passed to TENxFileList; otherwise, not used.
con	The connection from which data is loaded or to which data is saved. If this is a character vector, it is assumed to be a file name and a corresponding file connection is created and then closed after exporting the object. If it is a BiocFile derivative, the data is loaded from or saved to the underlying resource. If missing, the function will return the output as a character vector, rather than writing to a connection.
text	If con is missing, this can be a character vector directly providing the string data to import.

Details

Note that one can provide a ref argument to import method which will get passed to the internal splitAltExps operation. This allows one to set a mainExpName in the output object.

Value

A SpatialExperiment object

Functions

• import(con = TENxXenium, format = ANY, text = ANY): Import Xenium Analyzer data

Slots

resources

A TENxFileList or TENxH5 object containing the cell feature matrix.

boundaries

Either a TENxSpatialParquet or TENxSpatialCSV object containing the spatial boundaries data.

coordNames

character() A vector specifying the names of the columns in the spatial data containing the spatial coordinates.

sampleId

character(1) A scalar specifying the sample identifier.

colData

TENxSpatialParquet A TENxSpatialParquet object containing the spatial coordinates data.

metadata

XeniumFile A XeniumFile object containing the metadata information.

See Also

https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/analysis/xoa-output-understanding-outputs

Examples

showClass("TENxXenium")

zipfile <- paste0(
    "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenDemo/",
    "Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip"
)
destfile <- XeniumIO:::.cache_url_file(zipfile)
outfold <- file.path(
    tempdir(), tools::file_path_sans_ext(basename(zipfile))
)
if (!dir.exists(outfold))
    dir.create(outfold, recursive = TRUE)
unzip(
    zipfile = destfile, exdir = outfold, overwrite = FALSE
)
TENxXenium(xeniumOut = outfold) |>
    import(ref = "Gene Expression")

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A minimal class to represent Xenium metadata

Description

This class is a minimal class to represent Xenium metadata. It is dedicated to importing experiment.xenium metadata files. It uses the jsonlite package to import the metadata.

Usage

XeniumFile(resource)

## S4 method for signature 'XeniumFile,ANY,ANY'
import(con, format, text, ...)

Arguments

resource	character(1) The path to the Xenium metadata file.
con	The connection from which data is loaded or to which data is saved. If this is a character vector, it is assumed to be a file name and a corresponding file connection is created and then closed after exporting the object. If it is a BiocFile derivative, the data is loaded from or saved to the underlying resource. If missing, the function will return the output as a character vector, rather than writing to a connection.
format	The format of the output. If missing and con is a file name, the format is derived from the file extension. This argument is unnecessary when con is a derivative of BiocFile.
text	If con is missing, this can be a character vector directly providing the string data to import.
...	Parameters to pass to the format-specific method.

Value

A XeniumFile object

Functions

• import(con = XeniumFile, format = ANY, text = ANY): Import Xenium metadata

Examples

showClass("XeniumFile")

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