2020
DOI: 10.1038/s10038-020-00851-4
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A review of UMAP in population genetics

Abstract: Uniform manifold approximation and projection (UMAP) has been rapidly adopted by the population genetics community to study population structure. It has become common in visualizing the ancestral composition of human genetic datasets, as well as searching for unique clusters of data, and for identifying geographic patterns. Here we give an overview of applications of UMAP in population genetics, provide recommendations for best practices, and offer insights on optimal uses for the technique.

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Cited by 112 publications
(100 citation statements)
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“…Our results demonstrating the advantages of semi-supervised reduction suggest such methods could be utilized to refine upper bounds on the dimension of transcriptomes, such as the dimensions necessary to separate cell type designations [56]. Moreover, these questions and results are relevant to multi-faceted datasets outside of single-cell genomics, such as in phylogenetics or population genetics, where UMAP/t-SNE are used to explore structure of genetic interactions and evolutionary relationships [57]. Our findings should also be of interest beyond the biological sciences, e.g.…”
Section: Discussionmentioning
confidence: 99%
“…Our results demonstrating the advantages of semi-supervised reduction suggest such methods could be utilized to refine upper bounds on the dimension of transcriptomes, such as the dimensions necessary to separate cell type designations [56]. Moreover, these questions and results are relevant to multi-faceted datasets outside of single-cell genomics, such as in phylogenetics or population genetics, where UMAP/t-SNE are used to explore structure of genetic interactions and evolutionary relationships [57]. Our findings should also be of interest beyond the biological sciences, e.g.…”
Section: Discussionmentioning
confidence: 99%
“…Fig. 2 demonstrates uniform manifold approximate and projection (UMAP) GSE154245 data set for quality control (QC) ( Diaz-Papkovich et al, 2021 ).
Fig.
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Section: Methodsmentioning
confidence: 99%
“…Secondly, remaining samples were projected onto a principal component analysis (PCA), calculated with an in-house European reference panel to calculate the 20 first principal components for each population. UMAP 54 was used to reduce the coordinates of test samples on 20 principal components to two dimensions. Additional European samples not in the original reference set were also projected onto the PCA and UMAP components to identify ancestries, and samples with Swedish ancestry were identified.…”
Section: Genotyping and Association Analysismentioning
confidence: 99%