spatialPlotClusters: Spatial coordinates plot visualization

In DR.SC: Joint Dimension Reduction and Spatial Clustering

Spatial coordinates plot visualization

Description

Intuitive way of visualizing how cell types changes across the spatial locations.

Usage

  spatialPlotClusters(seu)

Arguments

seu	an object of class "Seurat" obtained by DR.SC.

Details

Nothing

Value

return a ggplot2 object.

Note

nothing

Author(s)

Wei Liu

References

None

See Also

None

Examples

## we generate the spatial transcriptomics data with lattice neighborhood, i.e. ST platform.
    seu <- gendata_RNAExp(height=10, width=10,p=50, K=4)
    library(Seurat)
    seu <- NormalizeData(seu)
    # choose spatially variable features using Seurat
    seu <- FindSVGs(seu)
    # use SVGs to fit DR.SC model
    # maxIter = 2 is only used for illustration, and user can use default.
    seu1 <- DR.SC(seu, K=4,platform = 'ST', maxIter=2,verbose=FALSE)
    spatialPlotClusters(seu1)

DR.SC documentation built on May 29, 2024, 2:12 a.m.