DR-SC.Rmd
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 4.1.3
#> Loading required package: spatstat.data
#> Warning: package 'spatstat.data' was built under R version 4.1.3
#> spatstat.geom 2.4-0
#> 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, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. 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.