Add analysis data from a 10x Genomics Visium experiment to a SPE object

This function adds to a SPE (SpatialExperiment-class) object the output from read10xVisiumAnalysis().

add10xVisiumAnalysis(spe, visium_analysis)

Arguments

spe

A SpatialExperiment-class object.

visium_analysis

The output from read10xVisiumAnalysis().

Value

A SpatialExperiment-class object with the clustering results from SpaceRanger added to colData(spe) and the dimension reduction results added to reducedDims(spe). Added data starts with the 10x_ prefix to make them easy to differentiate.

Details

You might want to use read10xVisiumWrapper() instead of using this function directly.

See also

Other Utility functions for reading data from SpaceRanger output by 10x Genomics: read10xVisiumAnalysis(), read10xVisiumWrapper()

Examples

## See 'Using spatialLIBD with 10x Genomics public datasets' for
## a full example using this function.
if (interactive()) {
    browseVignettes(package = "spatialLIBD")
}

## Note that ?SpatialExperiment::read10xVisium doesn't include all the files
## we need to illustrate read10xVisiumWrapper().