Clustering trees: a visualization for evaluating clusterings at multiple resolutions
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Abstract
Clustering techniques are widely used in the analysis of large datasets to group together samples with similar properties. For example, clustering is often used in the field of single-cell RNA-sequencing in order to identify different cell types present in a tissue sample. There are many algorithms for performing clustering, and the results can vary substantially. In particular, the number of groups present in a dataset is often unknown, and the number of clusters identified by an algorithm can change based on the parameters used. To explore and examine the impact of varying clustering resolution, we present clustering trees. This visualization shows the relationships between clusters at multiple resolutions, allowing researchers to see how samples move as the number of clusters increases. In addition, meta-information can be overlaid on the tree to inform the choice of resolution and guide in identification of clusters. We illustrate the features of clustering trees using a series of simulations as well as two real examples, the classical iris dataset and a complex single-cell RNA-sequencing dataset. Clustering trees can be produced using the clustree R package, available from CRAN and developed on GitHub.
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Now published in GigaScience doi: 10.1093/gigascience/giy083
Luke Zappia 1Bioinformatics, Murdoch Children’s Research Institute2School of Biosciences, University of MelbourneFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luke ZappiaAlicia Oshlack 1Bioinformatics, Murdoch Children’s Research Institute2School of Biosciences, University of MelbourneFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alicia Oshlack
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy083 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101…
Now published in GigaScience doi: 10.1093/gigascience/giy083
Luke Zappia 1Bioinformatics, Murdoch Children’s Research Institute2School of Biosciences, University of MelbourneFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luke ZappiaAlicia Oshlack 1Bioinformatics, Murdoch Children’s Research Institute2School of Biosciences, University of MelbourneFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alicia Oshlack
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy083 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101258 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101259 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101260
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