performUMAP {scDataviz} | R Documentation |
SingleCellExperiment
object, using the basic R implementation of UMAP.Perform UMAP on an input data-frame or matrix, or SingleCellExperiment
object, using the basic R implementation of UMAP.
performUMAP( indata, config = NULL, assay = "scaled", reducedDim = NULL, dims = seq_len(20), newDimName = NULL, useMarkers = NULL, verbose = TRUE )
indata |
A data-frame or matrix, or |
config |
UMAP configuration settings |
assay |
Name of the assay slot in |
reducedDim |
A dimensional reduction / embedding stored within
|
dims |
If 'reducedDim' is activated, the number of dimensions to use. |
newDimName |
Name for the new dimensional embedding that will be produced.
If nothing is selected for neither this nor |
useMarkers |
Before performing UMAP, subset the data for these markers. |
verbose |
Boolean (TRUE / FALSE) to print messages to console or not. |
Perform UMAP on an input data-frame or matrix, or SingleCellExperiment
object, using the basic R implementation of UMAP.
A SingleCellExperiment
object.
Kevin Blighe <kevin@clinicalbioinformatics.co.uk>
# create random data that follows a negative binomial mat <- jitter(matrix( MASS::rnegbin(rexp(1000, rate=.1), theta = 4.5), ncol = 20)) colnames(mat) <- paste0('CD', 1:ncol(mat)) performUMAP(mat)