read10xVisium {SpatialExperiment} | R Documentation

## Load data from a 10x Genomics Visium experiment

### Description

Creates a `SpatialExperiment` from the Space Ranger output directories for 10x Genomics Visium spatial gene expression data.

### Usage

    read10xVisium(
      samples = "",
      sample_id = paste0("sample", sprintf("%02d", seq_along(samples))),
      type = c("HDF5", "sparse"),
      data = c("filtered", "raw"),
      images = "lowres",
      load = TRUE
    )

### Arguments

`samples` | a character vector specifying one or more directories, each corresponding to a 10x Genomics Visium sample (see details); if provided, names will be used as sample identifiers
`sample_id` | character string specifying unique sample identifiers, one for each directory specified via `samples`; ignored if `!is.null(names(samples))`
`type` | character string specifying the type of format to read count data from (see `read10xCounts`)
`data` | character string specifying whether to read in filtered (spots mapped to tissue) or raw data (all spots).
`images` | character vector specifying which images to include. Valid values are `"lowres", "hires", "fullres", "detected", "aligned"`
`load` | logical; should the image(s) be loaded into memory as a `grob`? If FALSE, will store the path/URL instead.

### Details

The constructor assumes data from each sample are located in a single output directory as returned by Space Ranger, thus having the following file organization:

sample
|—outs
· · |—raw/filtered_feature_bc_matrix.h5
· · |—raw/filtered_feature_bc_matrix
· · · · |—barcodes.tsv
· · · · |—features.tsv
· · · · |—matrix.mtx
· · |—spatial
· · · · |—scalefactors_json.json
· · · · |—tissue_lowres_image.png
· · · · |—tissue_positions_list.csv

### Value

a `SpatialExperiment` object

### Author(s)

Helena L. Crowell

### Examples

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

    sample_ids <- c("section1", "section2")
    samples <- file.path(dir, sample_ids)

    list.files(samples[1])
    list.files(file.path(samples[1], "spatial"))
    file.path(samples[1], "raw_feature_bc_matrix")

    (spe <- read10xVisium(samples, sample_ids,
      type = "sparse", data = "raw",
      images = "lowres", load = FALSE))

    # tabulate number of spots mapped to tissue
    cd <- colData(spe, spatialData = TRUE)
    table(
      in_tissue = cd$in_tissue,
      sample_id = cd$sample_id)

    # view available images
    imgData(spe)

[Package SpatialExperiment version 1.4.0 Index]