Quick and dirty way of using UMAP in R using rPyhton
#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]) |
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