Dendrogram Explained

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.^[2]
• in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree.^[3]

The name dendrogram derives from the two ancient greek words, meaning "tree", and, meaning "drawing, mathematical figure".^{[4] [5]}

Clustering example

For a clustering example, suppose that five taxa (

a to e ) have been clustered by UPGMA based on a matrix of genetic distances. The hierarchical clustering dendrogram would show a column of five nodes representing the initial data (here individual taxa), 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 nodes on the right representing individual observations all plotted at zero height).

See also

• Cladogram
• Distance matrices in phylogeny
• Hierarchical clustering
• MEGA, a freeware for drawing dendrograms
• yEd, a freeware for drawing and automatically arranging dendrograms
• Taxonomy

References

Sources

• Galili . T. . 2015 . dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering . 10.1093/bioinformatics/btv428 . Bioinformatics . 31 . 22 . 3718–3720 . 26209431 . 4817050 .

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).

Notes and References

1. Book: Everitt, Brian . 1998 . Dictionary of Statistics . Cambridge, UK . Cambridge University Press . 96 . 0-521-59346-8 . registration .
2. Wilkinson. Leland. Friendly. Michael. The History of the Cluster Heat Map. The American Statistician. May 2009. 63. 2. 179–184. 10.1198/tas.2009.0033. 122792460. 10.1.1.165.7924.
3. Encyclopedia: Phylogenetic tree (biology). Encyclopedia Britannica. 2018-10-22. en.
4. Book: Bailly, Anatole . Abrégé du dictionnaire grec français . 1981-01-01 . Hachette . 2010035283 . Paris . 461974285 .
5. Web site: Greek-french dictionary online . Bailly . Anatole . www.tabularium.be . October 20, 2018.