Combine two or more modalities dimensionality reductions.

This function will combine two or more modalities dimensionality reductions into a single reduction.

addCombinedDims(
  ArchRProj = NULL,
  name = "CombinedDims",
  reducedDims = NULL,
  dimWeights = NULL,
  dimsToUse = NULL,
  scaleDims = NULL,
  corCutOff = 0.75
)

Arguments

ArchRProj

An ArchRProject object.

name

The name for the combinedDims to be stored as.

reducedDims

The name of the reducedDims objects (i.e. "IterativeLSI") to use from the designated ArchRProject.

dimWeights

A vector of weights to be used to weight each dimensionality reduction when combining.

dimsToUse

A vector containing the dimensions from the reducedDims objects to use.

scaleDims

A boolean value that indicates whether to z-score the reduced dimensions for each cell. This is useful for minimizing the contribution of strong biases (dominating early PCs) and lowly abundant populations. However, this may lead to stronger sample-specific biases since it is over-weighting latent PCs. If set to NULL this will scale the dimensions based on the value of scaleDims when the reducedDims were originally created during dimensionality reduction. This idea was introduced by Timothy Stuart.

corCutOff

A numeric cutoff for the correlation of each dimension to the sequencing depth. If the dimension has a correlation to sequencing depth that is greater than the corCutOff, it will be excluded from analysis.