performUMAP {scDataviz} | R Documentation

## Perform UMAP on an input data-frame or matrix, or `SingleCellExperiment` object, using the basic R implementation of UMAP.

### Description

Perform UMAP on an input data-frame or matrix, or `SingleCellExperiment` object, using the basic R implementation of UMAP.

### Usage

    performUMAP(
      indata,
      config = NULL,
      assay = "scaled",
      reducedDim = NULL,
      dims = seq_len(20),
      newDimName = NULL,
      useMarkers = NULL,
      verbose = TRUE
    )

### Arguments

`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.

### Details

Perform UMAP on an input data-frame or matrix, or `SingleCellExperiment` object, using the basic R implementation of UMAP.

### Value

A `SingleCellExperiment` object.

### Author(s)

Kevin Blighe <kevin@clinicalbioinformatics.co.uk>

### Examples

    # 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)

[Package scDataviz version 1.0.0 Index]