R - DBSCAN fviz_cluster - 使用dim1 和dim2 获取元素的坐标

Question

I'm a noob with R, and I'm trying to do clustering on some data samples. I've tried a PCA,

res.pca <- PCA(df, 
               ncp = 5, # nb composantes principales.
               graph = TRUE,
               )

and I can get the full elements list with new coordinates using

res.pca$ind

This is great and works perfectly for info using the 2 first axis with the PCA, I've 80% of variability on one axis and a bit more than 10% on the Second axis. I was quite proud of the result considering that I've 30 variables ... and in the End the PCA implicitly says that 2 dimension will be enough.

Still working on those data I tried the DBSCAN Clustering method fpc::dbscan :

library (factoextra)
db <- fpc::dbscan(df, eps = 22, MinPts = 3)

and after doing the dbscan and graphing the clusters using fviz_cluster, the Two dimensions display says : 92.8% on axis 1 and 6.7% on axis 2!!!! (more than 99% of the total variance explained with 2 axis !

In short, the DBSCAN has transformed my 30 variables data in a way that looks to be better than the PCA. The overall clustering of DBSCAN is rubbish for my data, but the transformation that has been used is absolutely excellent.

My issue is that I would like to get access to those new coordinates ... but no way at this time... the only accessible variables I can see are : db$cluster, db$eps, db$Minpts, db$isseed

BUT I suspect that some data are accessible otherwize how fviz_cluster, could present the data.

Any Idea ?

Answer 1

The projection is not done by dbscan. fviz_cluster uses the first two components obtained via stats::prcomp on the data.