r UMAP

Posted 2021-05-23

#install UMAP from https://github.com/lmcinnes/umap
#install.packages("rPython")

umap <- function(x,n_neighbors=10,n_components=2,min_dist=0.1,metric="euclidean"){
  x <- as.matrix(x)
  colnames(x) <- NULL
  rPython::python.exec( c( "def umap(data,n,d,mdist,metric):",
                           "\timport umap" ,
                           "\timport numpy",
                           "\tembedding = umap.UMAP(n_neighbors=n,n_components=d,min_dist=mdist,metric=metric).fit_transform(data)",
                           "\tres = embedding.tolist()",
                           "\treturn res"))
  
  res <- rPython::python.call( "umap", x,n_neighbors,n_components,min_dist,metric)
  do.call("rbind",res)
}

data(iris)
res <- umap(iris[,1:4])