read10xVisium: Load data from a 10x Genomics Visium experiment

In drighelli/VisiumExperiment: S4 Class for Spatially Resolved -omics Data

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 (where "raw/filtered" refers to either "raw" or "filtered" to match the 'data' argument.) The base directory "outs/" from Space Ranger can either be included manually in the paths provided in 'samples', or can be ignored; if ignored, it will be added automatically. The '.h5' files are used if 'type = "HDF5"'. (Note that 'tissue_positions.csv' was renamed in Space Ranger v2.0.0.)

sample
· | — outs
· · | — raw/filtered_feature_bc_matrix.h5
· · | — raw/filtered_feature_bc_matrix
· · · | — barcodes.tsv.gz
· · · | — features.tsv.gz
· · · | — matrix.mtx.gz
· · | — spatial
· · · | — scalefactors_json.json
· · · | — tissue_lowres_image.png
· · · | — tissue_positions.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, "outs")
  
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))

# base directory 'outs/' from Space Ranger can also be omitted
samples2 <- file.path(dir, sample_ids)
(spe2 <- read10xVisium(samples2, sample_ids, 
  type = "sparse", data = "raw", 
  images = "lowres", load = FALSE))

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

# view available images
imgData(spe)

drighelli/VisiumExperiment documentation built on June 30, 2024, 10:55 a.m.