readVisium {BayesSpace} | R Documentation

## Load a Visium spatial dataset as a SingleCellExperiment.

### 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)

[Package BayesSpace version 1.4.1 Index]