recalculate.embeddings: Recalculate low dimensional embeddings after projection

In carmonalab/ProjecTILs: Reference-based analysis of scRNA-seq data

Recalculate low dimensional embeddings after projection

Description

Given a reference object and a (list of) projected objects, recalculate low-dim embeddings accounting for the projected cells

Usage

recalculate.embeddings(
  ref,
  projected,
  ref.assay = "integrated",
  proj.assay = "integrated",
  ndim = NULL,
  n.neighbors = 20,
  min.dist = 0.3,
  recalc.pca = FALSE,
  resol = 0.4,
  k.param = 15,
  metric = "cosine",
  umap.method = c("umap", "uwot"),
  seed = 123
)

Arguments

ref	Reference map
projected	A projected object (or list of projected objects) generated using make.projection
ref.assay	Assay for reference object
proj.assay	Assay for projected object(s)
ndim	Number of dimensions for recalculating dimensionality reductions
n.neighbors	Number of neighbors for UMAP algorithm
min.dist	Tightness parameter for UMAP embedding
recalc.pca	Whether to recalculate the PCA embeddings with the combined reference and projected data
resol	Resolution for unsupervised clustering
k.param	Number of nearest neighbors for clustering
metric	Distance metric to use to find nearest neighbors for UMAP
umap.method	Which method should be used to calculate UMAP embeddings
seed	Random seed for reproducibility

Value

A combined reference object of reference and projected object(s), with new low dimensional embeddings

Examples

combined <- recalculate.embeddings(ref, projected, ndim=10)

carmonalab/ProjecTILs documentation built on April 13, 2025, 10:04 p.m.