Retrieve dimension reduction embedding and object using UMAP
# S4 method for DsATACsc dimRed_UMAP( .object, regions, tfidf = TRUE, pcs = 1:50, normPcs = FALSE, umapParams = list(distMethod = "euclidean", min_dist = 0.5, n_neighbors = 25), rmDepthCor = 1 )
character string specifying the region type to retrieve the UMAP coordinates from.
GRanges object specifying coordinates that fragment counts
will be aggregated over
normalize the counts using TF-IDF transformation
components to use to compute the SVD
flag indicating whether to apply z-score normalization to PCs for each cell
parameters to compute UMAP coordinates (passed on to
muRtools::getDimRedCoords.umap and further to
correlation cutoff to be used to discard principal components associated with fragment depth (all iterationa). By default (value >=1) no filtering will be applied.
S3 object containing dimensionality reduction results
The output object includes the final singular values/principal components (
result$pcaCoord), the low-dimensional coordinates (
result$umapCoord) as well as region set that provided the basis for the dimension reduction (