celdaUmap {celda} | R Documentation |
Embeds cells in two dimensions using umap.
celdaUmap( counts, celdaMod, maxCells = NULL, minClusterSize = 100, modules = NULL, seed = 12345, ... )
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' |
A two column matrix of UMAP coordinates#' @examples data(celdaCGSim, celdaCGMod) umapRes <- celdaUmap(celdaCGSim$counts, celdaCGMod)