read10xVisium {SpatialExperiment} | R Documentation |
Creates a SpatialExperiment
from the Space Ranger
output directories for 10x Genomics Visium spatial gene expression data.
read10xVisium( samples = "", sample_id = paste0("sample", sprintf("%02d", seq_along(samples))), type = c("HDF5", "sparse"), data = c("filtered", "raw"), images = "lowres", load = TRUE )
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 |
type |
character string specifying
the type of format to read count data from
(see |
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 |
load |
logical; should the image(s) be loaded into memory
as a |
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
a SpatialExperiment
object
Helena L. Crowell
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)