This vignette provides an introduction to the R package DR.SC, where the function DR.SC implements the model DR-SC, spatial clustering with hidden Markov random field using empirical Bayes. The package can be installed with the following command from Github:
install.packages('remotes') remotes::install_github("feiyoung/DR.SC")
or install from CRAN
install.packages("DR.SC")
The package can be loaded with the command:
library("DR.SC")
#> Loading required package: parallel
#> Loading required package: spatstat.geom
#> Warning: package 'spatstat.geom' was built under R version 4.0.5
#> Loading required package: spatstat.data
#> Warning: package 'spatstat.data' was built under R version 4.0.4
#> spatstat.geom 2.3-0
#> Warning in register(): Can't find generic `scale_type` in package ggplot2 to
#> register S3 method.
#> DR.SC : Joint dimension reduction and spatial clustering is conducted for
#> Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
#> Wei Liu, Xu Liao, Xiang Zhou, Shijie Shi and Jin Liu. (2021) <doi:10.1101/2021.12.25.474153>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.