add10xVisiumAnalysis: Add analysis data from a 10x Genomics Visium experiment to a...

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

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

Description

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

Usage

add10xVisiumAnalysis(spe, visium_analysis)

Arguments

spe	A SpatialExperiment-class object.
visium_analysis	The output from read10xVisiumAnalysis().

Details

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

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.

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().

LieberInstitute/spatialLIBD documentation built on Dec. 19, 2024, 7:12 p.m.