getReducedDims | R Documentation |
This function gets a dimensionality reduction object (i.e. UMAP, tSNE, etc) from a given ArchRProject.
getReducedDims(
ArchRProj = NULL,
reducedDims = "IterativeLSI",
returnMatrix = TRUE,
dimsToUse = NULL,
scaleDims = NULL,
corCutOff = 0.75
)
ArchRProj |
An |
reducedDims |
The name of the |
returnMatrix |
If set to "mat" or "matrix", the function will return the |
dimsToUse |
A vector containing the dimensions (i.e. 1:30) to return from the |
scaleDims |
A boolean describing 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 |
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 |
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