projectUMAP: Project cells into a reduced embedding with UMAP

In plantformatics/Socrates: Analysis of scATAC-seq data

Project cells into a reduced embedding with UMAP

Description

Project cells into a reduced embedding with UMAP

Usage

projectUMAP(
  obj,
  m.dist = 0.01,
  k.near = 40,
  metric = "cosine",
  svd_slotName = "PCA",
  umap_slotName = "UMAP",
  verbose = FALSE,
  seed = 1
)

Arguments

obj	list, object containing 'PCA' for projecting into a reduced embedding with UMAP.
m.dist	numeric, m_dist parameter for uwot::umap. Defaults to 0.1
k.near	numeric, k-nearest neighbors used by the uwot::umap algorithm. Defaults to 15.
metric	character, distance metric used by uwot::umap. Defaults to cosine.
svd_slotName	character, name of desired svd_slotName for running UMAP. Defaults to "PCA".
umap_slotName	character, name of desired umap_slotName for return UMAP results. Defaults to "UMAP".
verbose	logical. Defaults to FALSE.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.