seurat2cloupe: Extract data to import to Loupe Cell Browser

In saisomesh2594/funcutils: Utility Functions

Description

This function extracts data from a given seurat object for import into Loupe Cell Browser. It generates two csv files - one containing the coordinates for all the cells for the reduction of interest and one containing meta-data information such as clusters, categories, etc.

Usage

seurat2cloupe(object, reduction, dims, metadata, keyword, opdir)

Arguments

object	A Seurat Object
reduction	The reduction to extract the coordinates for. 'tsne' or 'umap'
dims	The number of dimensions to extract for a give reduction
metadata	The column name in the seurat object metadata table to extract
keyword	A keyword for the filename
opdir	The output directory in which the files will be written

Value

Two .csv files written to the specified output directory - data4cloupe_keyword.csv contains the reduction coordinates and cluster4cloupe_keyword.csv contains the metadata information.

saisomesh2594/funcutils documentation built on Sept. 2, 2020, 12:39 p.m.