Abstract The t-distributed stochastic neighbor embedding (t-SNE) method is one of the leading techniques for data visualization and clustering. This method finds lower-dimensional embedding of data points while minimizing distortions in distances between neighboring data points. By construction, t-SNE discards information about large-scale structure of the data. We show that adding a global cost function to the t-SNE cost function makes it possible to cluster the data while preserving global intercluster data structure. We test the new global t-SNE (g-SNE) method on one synthetic and two real data sets on flower shapes and human brain cells. We find that significant and meaningful global structure exists in both the plant and human brain data sets. In all cases, g-SNE outperforms t-SNE and UMAP in preserving the global structure. Topological analysis of the clustering result makes it possible to find an appropriate trade-off of data distribution across scales. We find differences in how data are distributed across scales between the two subjects that were part of the human brain data set. Thus, by striving to produce both accurate clustering and positioning between clusters, the g-SNE method can identify new aspects of data organization across scales.
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Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data
The rapid development of scRNA-seq technologies enables us to explore the transcriptome at the cell level on a large scale. Recently, various computational methods have been developed to analyze the scRNAseq data, such as clustering and visualization. However, current visualization methods, including t-SNE and UMAP, are challenged by the limited accuracy of rendering the geometric relationship of populations with distinct functional states. Most visualization methods are unsupervised, leaving out information from the clustering results or given labels. This leads to the inaccurate depiction of the distances between the bona fide functional states. In particular, UMAP and t-SNE are not optimal to preserve the global geometric structure. They may result in a contradiction that clusters with near distance in the embedded dimensions are in fact further away in the original dimensions. Besides, UMAP and t-SNE cannot track the variance of clusters. Through the embedding of t-SNE and UMAP, the variance of a cluster is not only associated with the true variance but also is proportional to the sample size.
We present supCPM, a robust supervised visualization method, which separates different clusters, preserves the global structure and tracks the cluster variance. Compared with six visualization methods using synthetic and real datasets, supCPM shows improved performance than other methods in preserving the global geometric structure and data variance. Overall, supCPM provides an enhanced visualization pipeline to assist the interpretation of functional transition and accurately depict population segregation.
The R package and source code are available at https://zenodo.org/record/5975977#.YgqR1PXMJjM.
Supplementary data are available at Bioinformatics online.
- Award ID(s):
- 2107215
- NSF-PAR ID:
- 10366634
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Bioinformatics
- Volume:
- 38
- Issue:
- 9
- ISSN:
- 1367-4803
- Format(s):
- Medium: X Size: p. 2496-2503
- Size(s):
- ["p. 2496-2503"]
- Sponsoring Org:
- National Science Foundation
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Supplementary information Supplementary data are available at Bioinformatics online.
