performUMAP: Perform UMAP on an input data-frame or matrix, or...
In kevinblighe/scDataviz: scDataviz: single cell dataviz and downstream analyses

Description Usage Arguments Details Value Author(s) Examples

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 `SingleCellExperiment` object. If a data-frame or matrix, only the derived co-ordinates for the first two dimensions are returned. If a `SingleCellExperiment` object, UMAP is performed on the assay named by `assay`, and the co-ordinates for the first two dimensions are stored as a reduced dimension named by `reducedDim`.
`config`	UMAP configuration settings
`assay`	Name of the assay slot in `indata` from which data will be taken, assuming `indata` is a `SingleCellExperiment` object.
`reducedDim`	A dimensional reduction / embedding stored within `indata`, e.g., PCA. If activated, UMAP will be performed on this object in place of the assay component specified by `assay`.
`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 `reducedDim`, then the new name will be `UMAP`. If nothing is selected for this, but, e.g., `PCA` is selected for `reducedDim`, then the new name will be `UMAP_PCA`.
`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)