CalculateUMAPSickleJr {jrSiCKLSNMF}

Calculate the UMAP for an object of class SickleJr

Description

Perform UMAP on the \mathbf{H} matrix alone (default) or within a modality by using UMAP on the W^vH corresponding to modality v.

Usage

CalculateUMAPSickleJr(
  SickleJr,
  umap.settings = umap::umap.defaults,
  modality = NULL
)

Arguments

SickleJr

An object of class SickleJr

umap.settings

Optional settings for the umap; defaults to umap.defaults

modality

A number corresponding to the desired modality; if set, will perform UMAP on \mathbf{W}^{\mathtt{modality}} on \mathbf{H} alone; not recommended for datasets of more than 1000 cells

Value

An object of class SickleJr with UMAP output based on the \mathbf{H} matrix alone or within a modality added to its umap slot

References

McInnes L, Healy J, Saul N, Großberger L (2018). “UMAP: Uniform Manifold Approximation and Projection.” Journal of Open Source Software, 3(29), 861. ISSN 2475-9066, doi:10.21105/JOSS.00861, https://joss.theoj.org/papers/10.21105/joss.00861.

Examples

#Since this example has only 10 observations,
#we need to modify the number of neighbors from the default of 15
umap.settings=umap::umap.defaults
umap.settings$n_neighbors=2
SimSickleJrSmall<-CalculateUMAPSickleJr(SimSickleJrSmall,
umap.settings=umap.settings)
SimSickleJrSmall<-CalculateUMAPSickleJr(SimSickleJrSmall,
umap.settings=umap.settings,modality=1)
SimSickleJrSmall<-CalculateUMAPSickleJr(SimSickleJrSmall,
umap.settings=umap.settings,modality=2)