umap_plot: Plot UMAP representation of a data set.

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Plot UMAP representation of a data set.

Description

UMAP (Uniform Manifold Approximation and Projection for Dimension Reduction) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. This function uses UMAP to represent the population structure of the data set (accnet or mash)

Usage

umap_plot(data, plot = TRUE, cluster, ...)

Arguments

data	An accnet or mash object
plot	print plot?
cluster	Two column data.frame with the nodes (column 1) and the cluster or classification(column 2)
...	Passed to uwot::umap function.

Value

A matrix of optimized coordinates.

References

McInnes, L, Healy, J, UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction, ArXiv e-prints 1802.03426, 2018

James Melville (2019). uwot: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction. R package version 0.1.4. https://CRAN.R-project.org/package=uwot

See Also

uwot

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.