ExportToCellbrowser: Export Seurat object for UCSC cell browser

In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description

Export Seurat object for UCSC cell browser

Usage

ExportToCellbrowser(object, dir, dataset.name = slot(object = object,
  name = "project.name"), reductions = "tsne", markers.file = NULL,
  cluster.field = "Cluster", cb.dir = NULL, port = NULL,
  skip.expr.matrix = FALSE, skip.metadata = FALSE,
  skip.reductions = FALSE, ...)

Arguments

object	Seurat object
dir	path to directory where to save exported files. These are: exprMatrix.tsv, tsne.coords.tsv, meta.tsv, markers.tsv and a default cellbrowser.conf
dataset.name	name of the dataset. Defaults to Seurat project name
reductions	vector of reduction names to export
markers.file	path to file with marker genes
cluster.field	name of the metadata field containing cell cluster
cb.dir	path to directory where to create UCSC cellbrowser static website content root, e.g. an index.html, .json files, etc. These files can be copied to any webserver. If this is specified, the cellbrowser package has to be accessible from R via reticulate.
port	on which port to run UCSC cellbrowser webserver after export
skip.expr.matrix	whether to skip exporting expression matrix
skip.metadata	whether to skip exporting metadata
skip.reductions	whether to skip exporting reductions
...	specifies the metadata fields to export. To supply field with human readable name, pass name as field="name" parameter.

Value

This function exports Seurat object as a set of tsv files to dir directory, copying the markers.file if it is passed. It also creates the default cellbrowser.conf in the directory. This directory could be read by cbBuild to create a static website viewer for the dataset. If cb.dir parameter is passed, the function runs cbBuild (if it is installed) to create this static website in cb.dir directory. If port parameter is passed, it also runs the webserver for that directory and opens a browser.

Author(s)

Maximilian Haeussler, Nikolay Markov

Examples

## Not run: 
ExportToCellbrowser(object = pbmc_small, dataset.name = "PBMC", dir = "out")

## End(Not run)

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.