View source: R/perform.scanorama.R
perform.scanorama | R Documentation |
Performs Scanorama integration on defined method-assays and reductions contained within. This is performed on reductions.
perform.scanorama( object, assay, slot = "norm.scaled", batch, n.dims = 50, reduction.save.suffix = "", batch_size = 5000, approx = TRUE, sigma = 15, alpha = 0.1, knn = 20, union = FALSE, verbose = FALSE, seed = 1234 )
object |
IBRAP S4 class object |
assay |
Character. String containing indicating which assay to use |
slot |
Character. String defining which slot in the assay to supply to Scanorama. Default = NULL |
batch |
Character. indicating the metadata column containing the batch to split the assay by. |
n.dims |
Numerical. The number of Scanorama dimensions to be produced. Default = 50 |
reduction.save.suffix |
Character. Should a suffix be added to the end of scanorama, This cannot include underscores. |
batch_size |
Numerical. The batch size used in the alignment vector computation. Useful when integrating large datasets. Default = 5000 |
approx |
Boolean. Use appoximate nearest neighbours within python, speeds up runtime. Default = TRUE |
sigma |
Numerical. Correction smoothing parameter on Gaussian kernel. Default = 15 |
alpha |
Numerical. Alignment score minimum cutoff. Default = 0.1 |
knn |
Numerical. Number of nearest neighbors to use for matching. Default = 20 |
verbose |
Logical Should function messages be printed? |
seed |
Numerical What seed should be set. Default = 1234 |
Scanorama reduction saved in the supplied method-assays
object <- perform.scanorama(object = object, assay = c('SCT', 'SCRAN', 'SCANPY'), slot = 'norm.scaled', batch = 'original.project', n.dims = 50)
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