Clustering trees: a visualization for evaluating clusterings at multiple resolutions
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.
Citation
@article{zappia2018,
author = {Zappia, Luke and Oshlack, Alicia},
title = {Clustering Trees: A Visualization for Evaluating Clusterings
at Multiple Resolutions},
journal = {GigaScience},
volume = {7},
number = {7},
date = {2018-07-01},
url = {https://lazappi.id.au/publications/2018-zappia-clustree},
doi = {10.1093/gigascience/giy083},
issn = {2047-217X},
langid = {en},
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.}
}