drscPlot: tNSE or UMAP plot visualization

In feiyoung/DR.SC: Joint Dimension Reduction and Spatial Clustering

tNSE or UMAP plot visualization

Description

Intuitive way of visualizing how cell types changes across the embeddings obatined by DR-SC.

Usage

  drscPlot(seu, dims=1:5, visu.method='tSNE',...)

Arguments

seu	an object of class "Seurat" obtained by DR.SC.
dims	a positive integer to specify the number of latent features for visualiztion.
visu.method	a string including 'tSNE' or "UMAP".
...	Other arguments passing to DimPlot function.

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
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)
drscPlot(seu1)

feiyoung/DR.SC documentation built on March 23, 2024, 6:31 p.m.