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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read10xVisium.R
\name{read10xVisium}
\alias{read10xVisium}
\title{Load data from a 10x Genomics Visium experiment}
\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{
\item{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}
\item{sample_id}{character string specifying unique sample identifiers,
one for each directory specified via \code{samples};
ignored if \code{!is.null(names(samples))}}
\item{type}{character string specifying
the type of format to read count data from
(see \code{read10xCounts})}
\item{data}{character string specifying whether to read in
filtered (spots mapped to tissue) or raw data (all spots).}
\item{images}{character vector specifying which images to include.
Valid values are \code{"lowres", "hires", "fullres", "detected", "aligned"}}
\item{load}{logical; should the image(s) be loaded into memory
as a \code{grob}? If FALSE, will store the path/URL instead.}
}
\value{
a \code{\link{SpatialExperiment}} object
}
\description{
Creates a \code{\link{SpatialExperiment}} from the Space Ranger
output directories for 10x Genomics Visium spatial gene expression data.
}
\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 \cr
· | — outs \cr
· · | — raw/filtered_feature_bc_matrix.h5 \cr
· · | — raw/filtered_feature_bc_matrix \cr
· · · | — barcodes.tsv.gz \cr
· · · | — features.tsv.gz \cr
· · · | — matrix.mtx.gz \cr
· · | — spatial \cr
· · · | — scalefactors_json.json \cr
· · · | — tissue_lowres_image.png \cr
· · · | — tissue_positions.csv \cr
}
\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)
}
\author{
Helena L. Crowell
}
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