Any reference can help for using the (dendrogram resulting from the hierarchical cluster analysis (HCA) and the principal component analysis (PCA), from a dataset which contains as much of the variance in the original data set as is possible, such as; to separate crude oils into their genetic groups.
To visualize the dendrogram generated by the hierarchical clustering, use the function fviz_dend() [factoextrapackage]
http://www.sthda.com/english/articles/31-principal-component-methods-in-r-practical-guide/117-hcpc-hierarchical-clustering-on-principal-components-essentials/
ggtree is good to visualize trees. Us the ape package to read in or convert your HCA tree object.
ggtree: https://bioconductor.org/packages/release/bioc/html/ggtree.html
ape: https://cran.r-project.org/web/packages/ape/ape.pdf
hclust function in R can help you out with (HCA). A small example.
https://github.com/immidikalipradeep/datamining/blob/master/hierarchical_clustering.R
Thank you;
Ajit Kumar Roy; Valentina Galata; Kali Pradeep
for your responses
Amer
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