Spatial coordinates plot visualization

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

spatialPlotClusters(seu)

Arguments

seu

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

Details

Nothing

Value

return a ggplot2 object.

References

None

Author

Wei Liu

Note

nothing

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)
#> Find the spatially variables genes by SPARK-X...
#> ## ===== SPARK-X INPUT INFORMATION ====
#> ## number of total samples: 100
#> ## number of total genes: 50
#> ## Running with single core, may take some time 
#> ## Testing With Projection Kernel
#> ## Testing With Gaussian Kernel 1
#> ## Testing With Gaussian Kernel 2
#> ## Testing With Gaussian Kernel 3
#> ## Testing With Gaussian Kernel 4
#> ## Testing With Gaussian Kernel 5
#> ## Testing With Cosine Kernel 1
#> ## Testing With Cosine Kernel 2
#> ## Testing With Cosine Kernel 3
#> ## Testing With Cosine Kernel 4
#> ## Testing With Cosine Kernel 5
    # 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)
#> Neighbors were identified for 100 out of 100 spots.
#> Fit DR-SC model...
#> Finish DR-SC model fitting
    spatialPlotClusters(seu1)