readVisium: Load a Visium spatial dataset as a SingleCellExperiment.

In BayesSpace: Clustering and Resolution Enhancement of Spatial Transcriptomes

Description

Load a Visium spatial dataset as a SingleCellExperiment.

Usage

readVisium(dirname)

Arguments

dirname

Path to spaceranger output directory (e.g. "sampleID/outs/"). This directory must contain the counts matrix and feature/barcode TSVs in filtered_feature_bc_matrix/, and the spot positions at spatial/tissue_positions_list.csv. (These are default locations for spaceranger outputs.)

Details

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.

Value

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.

Examples

## Not run: 
sce <- readVisium("path/to/outs/")

## End(Not run)

BayesSpace documentation built on Nov. 8, 2020, 8:03 p.m.