dimRed_UMAP,DsATACsc-method | R Documentation |
Retrieve dimension reduction embedding and object using UMAP
## S4 method for signature '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
)
.object |
|
regions |
character string specifying the region type to retrieve the UMAP coordinates from.
Alternatively, a |
tfidf |
normalize the counts using TF-IDF transformation |
pcs |
components to use to compute the SVD |
normPcs |
flag indicating whether to apply z-score normalization to PCs for each cell |
umapParams |
parameters to compute UMAP coordinates (passed on to
|
rmDepthCor |
correlation cutoff to be used to discard principal components associated with fragment depth (all iterationa). By default (value >=1) no filtering will be applied. |
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 (result$regionGr
).
an S3
object containing dimensionality reduction results
Fabian Mueller
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