mbicPlot: MBIC plot visualization

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

MBIC plot visualization

Description

Intuitive way of visualizing how modified BIC values changes across different number of clusters

Usage

  mbicPlot(seu, criteria="MBIC")

Arguments

seu	an object of class Seurat revised by DR.SC with argument K=NULL.
criteria	a string specifying the information criteria such as AIC, BIC and MBIC to be plotted, default as MBIC.

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=20, width=20,p=100, K=4)
  library(Seurat)
  seu <- NormalizeData(seu)
  # choose spatially variable features
  seu <- FindSVGs(seu)
  ## Just for illustrating the usage of mbicPlot
  seu[["RNA"]]@misc[['icMat']] <- data.frame(K=2:5, MBIC=c(105, 101, 99, 108))
  mbicPlot(seu)

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