celdaUmap: Embeds cells in two dimensions using umap.

Description Usage Arguments Value

Description

Embeds cells in two dimensions using umap.

Usage

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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)


celda documentation built on June 9, 2020, 2 a.m.