Package 'VisiumIO' reference manual

Title:	Import Visium data from the 10X Space Ranger pipeline
Description:	The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.
Authors:	Marcel Ramos [aut, cre]
Maintainer:	Marcel Ramos <[email protected]>
License:	Artistic-2.0
Version:	1.1.0
Built:	2024-06-30 03:27:04 UTC
Source:	https://github.com/bioc/VisiumIO

Represent and import spatial CSV data from 10X Genomics

Description

TENxSpatialCSV is a class to represent and import spatial CSV files with specific column names. It is a composed class of TENxIO::TENxFile and contains additional slots for the column names and whether the CSV is a list-type of file.

Usage

TENxSpatialCSV(resource, colnames = .TISSUE_POS_COLS)

## S4 method for signature 'TENxSpatialCSV,ANY,ANY'
import(con, format, text, ...)
TENxSpatialCSV(resource, colnames = .TISSUE_POS_COLS)

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

Arguments

`resource`	character(1) The path to the file
`colnames`	`character()` A vector specifying the column names of the CSV, defaults to `c("barcode", "in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres")`.
`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.
`...`	Additional inputs to the low level class generator functions

Details

Typically, the user will not create an object of this class directly but rather use the TENxVisium() constructor function to create an object of this class in the background. The column names are set to the default values of c("barcode", "in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres"). The column names can be changed by specifying the colnames argument in the constructor function.

Value

TENxSpatialCSV: An object of class TENxSpatialCSV

import-method: A DataFrame object containing the data from the CSV file

Slots

isList: logical(1) A scalar specifying whether the CSV is a list-type of file
colnames: character() A vector specifying the column names of the CSV

Examples

sample_dir <- system.file(
    file.path("extdata", "10xVisium", "section1"),
    package = "SpatialExperiment"
)
spatial_dir <- Filter(
  function(x) endsWith(x, "spatial"), list.dirs(sample_dir)
)
csvresource <- file.path(spatial_dir, "tissue_positions_list.csv")
TENxSpatialCSV(csvresource)
head(import(TENxSpatialCSV(csvresource)), 4)

sample_dir <- system.file(
    file.path("extdata", "10xVisium", "section1"),
    package = "SpatialExperiment"
)
spatial_dir <- Filter(
  function(x) endsWith(x, "spatial"), list.dirs(sample_dir)
)
csvresource <- file.path(spatial_dir, "tissue_positions_list.csv")
TENxSpatialCSV(csvresource)
head(import(TENxSpatialCSV(csvresource)), 4)

A class to represent and import spatial Visium data

Description

This class is a composed class of TENxFileList, which can contain a list of TENxFile objects, and a TENxSpatialList object. It is meant to handle spatial Visium data from 10X Genomics.

Usage

TENxSpatialList(
  resources,
  sample_id = "sample01",
  images = c("lowres", "hires", "detected", "aligned"),
  jsonFile = .SCALE_JSON_FILE,
  tissuePattern = "tissue_positions.*\\.csv",
  ...
)

## S4 method for signature 'TENxSpatialList,ANY,ANY'
import(con, format, text, ...)
TENxSpatialList(
  resources,
  sample_id = "sample01",
  images = c("lowres", "hires", "detected", "aligned"),
  jsonFile = .SCALE_JSON_FILE,
  tissuePattern = "tissue_positions.*\\.csv",
  ...
)

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

Arguments

`resources`	A TENxFileList object or a file path to the tarball containing the matrix / assay data resources.
`sample_id`	`character(1)` A single string specifying the sample ID.
`images`	`character()` A vector specifying the images to be imported; can be one or multiple of "lowres", "hires", "detected", "aligned".
`jsonFile`	`character(1)` A single string specifying the name of the JSON file containing the scale factors.
`tissuePattern`	`character(1)` A single string specifying the pattern to match the tissue positions file.
`...`	Parameters to pass to the format-specific method.
`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.

Details

Typically, the user will not create an object of this class directly but rather use the TENxVisium() constructor function to create an object of this class.

Value

A SpatialExperiment object

Methods (by generic)

import(con = TENxSpatialList, format = ANY, text = ANY): Import a TENxSpatialList object

Examples


spatial_dir <- system.file(
    file.path("extdata", "10xVisium", "section1", "outs", "spatial"),
    package = "SpatialExperiment"
)

TENxSpatialList(resources = spatial_dir)

spatial_dir <- system.file(
    file.path("extdata", "10xVisium", "section1", "outs", "spatial"),
    package = "SpatialExperiment"
)

TENxSpatialList(resources = spatial_dir)

A class to represent and import a single Visium Sample

Description

This class is a composed class of TENxFileList which can contain a list of TENxFile objects and a TENxSpatialList object. It is meant to handle a single Visium sample from 10X Genomics.

Usage

TENxVisium(
  resources,
  spatialResource,
  spacerangerOut,
  sample_id = "sample01",
  processing = c("filtered", "raw"),
  images = c("lowres", "hires", "detected", "aligned"),
  jsonFile = .SCALE_JSON_FILE,
  tissuePattern = "tissue_positions.*\\.csv",
  spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"),
  ...
)

## S4 method for signature 'TENxVisium,ANY,ANY'
import(con, format, text, ...)
TENxVisium(
  resources,
  spatialResource,
  spacerangerOut,
  sample_id = "sample01",
  processing = c("filtered", "raw"),
  images = c("lowres", "hires", "detected", "aligned"),
  jsonFile = .SCALE_JSON_FILE,
  tissuePattern = "tissue_positions.*\\.csv",
  spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"),
  ...
)

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

Arguments

`resources`	A TENxFileList object or a file path to the tarball containing the matrix / assay data resources.
`spatialResource`	A TENxSpatialList object or a file path to the tarball containing the spatial data.
`spacerangerOut`	`character(1)` A single string specifying the path to the sample directory of `⁠spaceranger count⁠`. The directory must contain the `⁠(processing)_feature_bc_matrix⁠` and `spatial` sub directories in addition to the `outs` folder.
`sample_id`	`character(1)` A single string specifying the sample ID.
`processing`	`character(1)` A single string indicating the processing folder available e.g., "filtered_feature_barcode_matrix" in the `spacerangerOut` folder. It can be either "filtered" or "raw" (default "filtered"). Only used when `spacerangerOut` is specified.
`images`	`character()` A vector specifying the images to be imported; can be one or multiple of "lowres", "hires", "detected", "aligned".
`jsonFile`	`character(1)` A single string specifying the name of the JSON file containing the scale factors.
`tissuePattern`	`character(1)` A single string specifying the pattern to match the tissue positions file.
`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.
`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.

Details

Typically, the user will not create an object of this class directly but rather use TENxVisiumList constructor function for multiple samples. Note that the images, jsonFile, tissuePattern, and spatialCoordsNames arguments are only considered when the spacerangerOut argument or both the resources and spatialResource arguments are paths to files.

Value

A SpatialExperiment object

Functions

import(con = TENxVisium, format = ANY, text = ANY): Import Visium data

Slots

resources: A TENxFileList object containing the Visium data.
spatialList: A TENxSpatialList object containing the spatial
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.

Examples


sample_dir <- system.file(
    file.path("extdata", "10xVisium", "section1"),
    package = "SpatialExperiment"
)

tv <- TENxVisium(
    spacerangerOut = sample_dir, processing = "raw", images = "lowres"
)

import(tv)

sample_dir <- system.file(
    file.path("extdata", "10xVisium", "section1"),
    package = "SpatialExperiment"
)

tv <- TENxVisium(
    spacerangerOut = sample_dir, processing = "raw", images = "lowres"
)

import(tv)

A class to represent and import multiple Visium samples

Description

This class contains a SimpleList of TENxVisium objects each corresponding to one sample.

Usage

TENxVisiumList(
  sampleFolders,
  sample_ids,
  processing = c("filtered", "raw"),
  images = c("lowres", "hires", "detected", "aligned"),
  jsonFile = .SCALE_JSON_FILE,
  tissuePattern = "tissue_positions.*\\.csv",
  spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"),
  ...
)

## S4 method for signature 'TENxVisiumList,ANY,ANY'
import(con, format, text, ...)
TENxVisiumList(
  sampleFolders,
  sample_ids,
  processing = c("filtered", "raw"),
  images = c("lowres", "hires", "detected", "aligned"),
  jsonFile = .SCALE_JSON_FILE,
  tissuePattern = "tissue_positions.*\\.csv",
  spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"),
  ...
)

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

Arguments

`sampleFolders`	`character()` A vector of strings specifying the directories containing the output of the `⁠spaceranger count⁠` command.
`sample_ids`	`character()` A vector of strings specifying the sample IDs. If not provided, the sample IDs will be the names of the `sampleFolders`. Therefore, the `sample_ids` must be the same length as `sampleFolders`.
`processing`	`character(1)` A single string indicating the processing folder available e.g., "filtered_feature_barcode_matrix" in the `spacerangerOut` folder. It can be either "filtered" or "raw" (default "filtered"). Only used when `spacerangerOut` is specified.
`images`	`character()` A vector specifying the images to be imported; can be one or multiple of "lowres", "hires", "detected", "aligned".
`jsonFile`	`character(1)` A single string specifying the name of the JSON file containing the scale factors.
`tissuePattern`	`character(1)` A single string specifying the pattern to match the tissue positions file.
`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.
`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.

Details

Typically, the user will provide a path to a directory containing the output of the ⁠spaceranger count⁠ command. The ⁠spaceranger count⁠ command outputs a folder containing the "raw" or "filtered" ⁠()_feature_bc_matrix⁠.

Value

A SpatialExperiment object

Functions

import(con = TENxVisiumList, format = ANY, text = ANY): Import multiple Visium samples

Examples


sample_dirs <- list.dirs(
    system.file(
        file.path("extdata", "10xVisium"),
        package = "SpatialExperiment"
    ),
    recursive = FALSE, full.names = TRUE
)

tvl <- TENxVisiumList(
    sampleFolders = sample_dirs,
    sample_ids = c("sample01", "sample02"),
    processing = "raw",
    images = "lowres"
)

import(tvl)

sample_dirs <- list.dirs(
    system.file(
        file.path("extdata", "10xVisium"),
        package = "SpatialExperiment"
    ),
    recursive = FALSE, full.names = TRUE
)

tvl <- TENxVisiumList(
    sampleFolders = sample_dirs,
    sample_ids = c("sample01", "sample02"),
    processing = "raw",
    images = "lowres"
)

import(tvl)

Package 'VisiumIO'

Help Index

Represent and import spatial CSV data from 10X Genomics

Description

Usage

Arguments

Details

Value

Slots

Examples

A class to represent and import spatial Visium data

Description

Usage

Arguments

Details

Value

Methods (by generic)

Examples

A class to represent and import a single Visium Sample

Description

Usage

Arguments

Details

Value

Functions

Slots

See Also

Examples

A class to represent and import multiple Visium samples

Description

Usage

Arguments

Details

Value

Functions

See Also

Examples