GeezerVison

GeezerVison is showing en.wikipedia.org — Dendrogram - Wikipedia

(Redirected from Dendrograms)

Not to be confused with Dendrogramma.

This article needs more citations. Please help improve this article by adding citations to reliable sources. Unsourced material may be challenged and removed.
Find sources: "Dendrogram" – news · newspapers · books · scholar · JSTOR (January 2017) (Learn how and when to remove this message)

Dendrogram of a hierarchical clustering (UPGMA) with the height of the nodes (adapted from bacterial 5S rRNA sequence data^[1]).

Dendrogram output for hierarchical clustering of marine provinces using presence / absence of sponge species.^[2]

A dendrogram of the Tree of Life. This phylogenetic tree is adapted from Woese et al. rRNA analysis.^[3] The vertical line at bottom represents the last universal common ancestor (LUCA).

Heatmap of RNA-Seq data showing two dendrograms in the left and top margins.

A dendrogram is a diagram representing a tree graph. This diagrammatic representation is frequently used in different contexts:

in hierarchical clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses.^[4]
in computational biology, it shows the clustering of genes or samples, sometimes in the margins of heatmaps.^[5]
in phylogenetics, it displays the evolutionary relationships among various biological taxa. In this case, the dendrogram is also called a phylogenetic tree.^[6]

The name dendrogram derives from the two ancient greek words δένδρον (déndron), meaning "tree", and γράμμα (grámma), meaning "drawing, mathematical figure".^[7]^[8]

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).

References

Citations

↑ Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996). "Phylogenetic inference". In Hillis DM, Moritz C, Mable BK (eds.). Molecular Systematics, 2nd edition. Sunderland, MA: Sinauer. pp. 407–514. ISBN 978-0-87893-282-5.
↑ Van Soest R, Boury-Esnault N, Vacelet J, Dohrmann M, Erpenbeck D, De Voogd N, Santodomingo N, Vanhoorne B, Kelly M, Hooper J (2012). "Global Diversity of Sponges (Porifera)". PLOS One. 7 (4) e35105. Bibcode:2012PLoSO...735105V. doi:10.1371/journal.pone.0035105. PMC 3338747. PMID 22558119.
↑ Woese, Carl R.; Kandler, O; Wheelis, M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya" (PDF). Proc Natl Acad Sci USA. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
↑ Everitt, Brian (1998). Dictionary of Statistics. Cambridge, UK: Cambridge University Press. p. 96. ISBN 0-521-59346-8.
↑ Wilkinson, Leland; Friendly, Michael (May 2009). "The History of the Cluster Heat Map". The American Statistician. 63 (2): 179–184. doi:10.1198/tas.2009.0033. S2CID 122792460.
↑ "Phylogenetic tree (biology)". Encyclopædia Britannica. Retrieved 2018-10-22.
↑ Bailly, Anatole (1981-01-01). Abrégé du dictionnaire grec français. Paris: Hachette. ISBN 2-01-003528-3. OCLC 461974285.
↑ Bailly, Anatole. "Greek-french dictionary online". tabularium.be. Archived from the original on March 18, 2022. Retrieved October 20, 2018.

Sources

Galili, T. (2015). "dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering". Bioinformatics. 31 (22): 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).

Retrieved from "https://en.wikipedia.org/w/index.php?title=Dendrogram&oldid=1385146451"

Categories:

Hidden categories: