runUMAP: Perform UMAP Dimensionality Reduction

In rliger: Linked Inference of Genomic Experimental Relationships

Perform UMAP Dimensionality Reduction

Description

Run UMAP on the aligned cell factors (result from alignFactors), or unaligned cell factors (raw result from runIntegration)) to generate a 2D embedding for visualization (or general dimensionality reduction). Has option to run on subset of factors. It is generally recommended to use this method for dimensionality reduction with extremely large datasets. The underlying UMAP calculation imports uwot umap.

Usage

runUMAP(
  object,
  useRaw = NULL,
  useDims = NULL,
  nDims = 2,
  distance = c("cosine", "euclidean", "manhattan", "hamming"),
  nNeighbors = 20,
  minDist = 0.1,
  dimredName = "UMAP",
  asDefault = NULL,
  seed = 42,
  verbose = getOption("ligerVerbose", TRUE),
  k = nDims,
  use.raw = useRaw,
  dims.use = useDims,
  n_neighbors = nNeighbors,
  min_dist = minDist,
  rand.seed = seed
)

Arguments

object	liger object with factorization results.
useRaw	Whether to use un-aligned cell factor loadings (H matrices). Default NULL search for aligned factor loadings first and un-aligned loadings then.
useDims	Index of factors to use for computing the embedding. Default NULL uses all factors.
nDims	Number of dimensions to reduce to. Default 2.
distance	Character. Metric used to measure distance in the input space. Default "cosine", alternative options include: "euclidean", "manhattan" and "hamming".
nNeighbors	Number of neighboring points used in local approximations of manifold structure. Default 20.
minDist	Numeric. Controls how tightly the embedding is allowed compress points together. Default 0.1.
dimredName	Name of the variable in cellMeta slot to store the result matrix. Default "UMAP".
asDefault	Logical, whether to set the resulting dimRed as default for visualization. Default NULL will set it when no default is set.
seed	Random seed for reproducibility. Default 42.
verbose	Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.
k, use.raw, dims.use, n_neighbors, min_dist, rand.seed	Deprecated. See Usage section for replacement.

Details

For nNeighbors, larger values will result in more global structure being preserved at the loss of detailed local structure. In general this parameter should often be in the range 5 to 50, with a choice of 10 to 15 being a sensible default.

For minDist, larger values ensure embedded points are more evenly distributed, while smaller values allow the algorithm to optimize more accurately with regard to local structure. Sensible values are in the range 0.001 to 0.5, with 0.1 being a reasonable default.

Value

The object where a "UMAP" variable is updated in the cellMeta slot with the whole 2D embedding matrix.

See Also

runTSNE

Examples

pbmc <- runUMAP(pbmcPlot)

rliger documentation built on Oct. 30, 2024, 1:07 a.m.