celdaUmap {celda} | R Documentation

## Embeds cells in two dimensions using umap.

### Description

Embeds cells in two dimensions using umap.

### Usage

    celdaUmap(
      counts,
      celdaMod,
      maxCells = NULL,
      minClusterSize = 100,
      modules = NULL,
      seed = 12345,
      ...
    )

### Arguments

`counts` | Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celdaMod'.
`celdaMod` | Celda object of class 'celda_CG'.
`maxCells` | Integer. Maximum number of cells to plot. Cells will be randomly subsampled if ncol(counts) > maxCells. Larger numbers of cells requires more memory. Default 25000.
`minClusterSize` | Integer. Do not subsample cell clusters below this threshold. Default 100.
`modules` | Integer vector. Determines which features modules to use for tSNE. If NULL, all modules will be used. Default NULL.
`seed` | Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made. the UMAP algorithm.
`...` | Additional parameters to 'uwot::umap'

### Value

A two column matrix of UMAP coordinates#' @examples data(celdaCGSim, celdaCGMod) umapRes <- celdaUmap(celdaCGSim$counts, celdaCGMod)

[Package celda version 1.3.4 Index]