Dendrogram
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A dendrogram is a diagram representing a tree. This diagrammatic representation is frequently used in different contexts:
- in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses.[1]
- in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heatmaps.
- in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree.
The name dendrogram derives from the two ancient greek words δένδρον (déndron), meaning "tree", and γράμμα (grámma), meaning "drawing, mathematical figure".[2][3]
Clustering example
For a clustering example, suppose this data is to be clustered using Euclidean distance as the distance metric.
The hierarchical clustering dendrogram would be as such:
The top row of nodes represents data (individual observations), and the remaining nodes represent the clusters to which the data belong, with the arrows representing the distance (dissimilarity).
The distance between merged clusters is monotone increasing with the level of the merger: the height of each node in the plot is proportional to the value of the intergroup dissimilarity between its two daughters (the top nodes representing individual observations are all plotted at zero height).
See also
- Cladogram
- Hierarchical clustering
- MEGA, a freeware for drawing dendrograms
- yEd, a freeware for drawing and automatically arranging dendrograms
- Distance matrices in phylogeny
References
- ^ Everitt, Brian (1998). Dictionary of Statistics. Cambridge, UK: Cambridge University Press. p. 96. ISBN 0-521-59346-8.
- ^ Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN 2010035283. OCLC 461974285.
- ^ Bailly, Anatole. "Greek-french dictionary online". www.tabularium.be. Retrieved October 20, 2018.
- Galili, T (2015). "dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering". Bioinformatics. 31: 3718–3720. doi:10.1093/bioinformatics/btv428. PMC 4817050. PMID 26209431.
External links
- Iris dendrogram - Example of using a dendrogram to visualize the 3 clusters from hierarchical clustering using the "complete" method vs the real species category (using R).