export_umap: Export UMAP embeddings from a Suerat object

In BrianLohman/SingleCellGarage: A collection of utilities to make working with (and combining) existing single cell packages easier

Description

Extract UMAP embedding from a Suerat object and write to file as csv By defult, writes two files, umap_embeddings.csv and clusters.csv for use in Loupe browser By default, drops a cell ID that is prefixed the cell barcode

Usage

export_umap(
  srt = srt,
  embeddings_file = "umap_embeddings.csv",
  cluster_id_file = "clusters.csv",
  Idents = NULL,
  drop_cell_ids = TRUE
)

Arguments

srt	A Seurat object
cluster_id_file	Name of csv file that containst he cluster IDs
Idents	Set the active Ident from Seurat metadata before exporting. Becomes grouping factor in clusters.csv. Default is active Ident.
drop_cell_ids	Drop the cell ID prefixed the the cell barcode by Seurat
umap_embeddings_file	Name of csv file that contains UMAP embeddings

Examples

## Not run: 
export_umap(srt = srt, embeddings_file = "umap_embeddings.csv", cluster_id_file = "clusters.csv",
    Idents = NULL, drop_cell_ids = TRUE)

## End(Not run)

BrianLohman/SingleCellGarage documentation built on Feb. 24, 2022, 4:58 a.m.