The vertical scale on the dendrogram represent the distance or dissimilarity. Each joining (fusion) of two clusters is represented on the diagram by the splitting of a vertical line into two vertical lines. The vertical position of the split, shown by a short bar gives the distance (dissimilarity) between the two clusters.
Cutting a dendrogram at a certain level gives a set of clusters. Cutting at another level gives another set of clusters. How would you pick where to cut the dendrogram? Is there something we could consider an optimal point? If I look at a dendrogram across time as it changes, should I cut at the same point?
I'm quite new to cluster analysis and I was trying to perform a hierarchical clustering algorithm (in R) on my data to spot some groups in my dataset. Initially, I tried with the k-means, with the ...
You've mixed two separate questions in one. Your 1st Q is actually about hierarchical cluster analysis, not dendrogram. (It is possible to do the HCA and save a range of cluster solutions and then choose the "best" one, - completely refraining from drawing the dendrogram.) Your second Q is about dendrogram, not HCA; moreover, that Q isn't quite clear, - can you be more specific: what bothers ...
I have dendrogram and a distance matrix. I wish to compute a heatmap -- without re-doing the distance matrix and clustering. Is there a function in R that permits this?
I have been using this dendrogram to visually identify clusters, and then clusters within the clusters, in order to understand product groupings. The process of manually identifying the clusters is time consuming, as I have dozens of matrices I need to do this to, so I'm looking for a method to automatically identify a sensible number of ...
I have viewed this clustering with an interactive dendrogram, but I want to understand how to interpret this better. A static view of my plot looks like this: The x-axis is all the genes with their index numbers 0-600 (the graph is quite big so sorry for the image quality).
Now to turn the resultant dendrogram into a number of groups of points (flat clusters), I want to choose which level to cut the tree at (the same as choosing the number of clusters).
In hierarchical clustering procedure, a distance matrix is used to construct a dendrogram with an appropriate method of clustering. In the process of constructing a dendrogram, a cophenetic matrix is computed.
