readVisium {BayesSpace} | R Documentation |
Load a Visium spatial dataset as a SingleCellExperiment.
readVisium(dirname)
dirname |
Path to spaceranger output directory (e.g. "sampleID/outs/").
This directory must contain the counts matrix and feature/barcode TSVs in
|
We store two variables associated with downstream BayesSpace
functions in a list called BayesSpace.data
in the
SingleCellExperiment's metadata
.
platform
is set to "Visium", and is used to determine spot
layout and neighborhood structure.
is.enhanced
is set to FALSE
to denote the object
contains spot-level data.
SingleCellExperiment containing the counts matrix in counts
and spatial data in colData
. Array coordinates for each spot are
stored in columns row
and col
, while image coordinates are
stored in columns imagerow
and imagecol
.
## Not run: sce <- readVisium("path/to/outs/") ## End(Not run)