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ExportToCellbrowser() exports a Seurat object as a UCSC Cell Browser dataset. It creates all required files (expression matrix, metadata, cell embeddings, marker genes) in the specified directory and optionally launches a local Cell Browser server.

​
Syntax

ExportToCellbrowser(
  object,
  dir,
  dataset.name = Project(object = object),
  reductions = NULL,
  markers.file = NULL,
  cluster.field = NULL,
  cb.dir = NULL,
  port = NULL,
  use.mtx = FALSE,
  meta.fields = NULL,
  meta.fields.names = NULL,
  matrix.slot = "counts",
  markers.n = 100,
  skip.markers = FALSE,
  skip.expr.matrix = FALSE,
  skip.metadata = FALSE,
  skip.reductions = FALSE
)

​
Parameters

​
object
Seurat
required
A Seurat object to export.
​
dir
character
required
Output directory where Cell Browser files will be written.
​
dataset.name
character
Name of the Cell Browser dataset. Defaults to Project(object).
​
reductions
character vector
default:"NULL"
Names of dimensional reductions to export. If NULL, exports all available reductions.
​
markers.file
character
default:"NULL"
Path to a pre-computed markers file. If NULL and skip.markers = FALSE, markers are computed automatically.
​
cluster.field
character
default:"NULL"
Metadata column to use as cell cluster labels.
​
cb.dir
character
default:"NULL"
If provided, also builds the Cell Browser HTML in this directory for direct serving.
​
port
integer
default:"NULL"
If provided, launches a local Cell Browser server on this port after export.
​
use.mtx
logical
default:"FALSE"
Export the expression matrix in .mtx.gz format (sparse). Automatically enabled for very large matrices.
​
meta.fields
character vector
default:"NULL"
Metadata columns to include. If NULL, all metadata columns are exported.
​
meta.fields.names
character vector
default:"NULL"
Display names for the metadata fields specified in meta.fields.
​
matrix.slot
character
default:"counts"
Which expression matrix to export. One of "counts", "data", or "scale.data".
​
markers.n
integer
default:"100"
Number of top markers per cluster to include in the exported markers file.
​
skip.markers
logical
default:"FALSE"
Skip marker gene computation and export.
​
skip.expr.matrix
logical
default:"FALSE"
Skip expression matrix export (for incremental updates).
​
skip.metadata
logical
default:"FALSE"
Skip metadata export.
​
skip.reductions
logical
default:"FALSE"
Skip dimensional reduction export.

​
Returns

Invisibly returns NULL. Creates the following files in dir:
  • exprMatrix.tsv.gz (or matrix.mtx.gz) — expression matrix
  • meta.tsv — cell metadata
  • <reduction>.coords.tsv.gz — cell coordinates for each reduction
  • markers.tsv — marker genes per cluster
  • cellbrowser.conf — Cell Browser configuration file

​
StopCellbrowser()

Stops a running Cell Browser server started by ExportToCellbrowser(). 
StopCellbrowser()

​
Examples

library(SeuratWrappers)

# Export only
ExportToCellbrowser(
  object = seurat_obj,
  dir = "cellbrowser_output",
  dataset.name = "PBMC_3k"
)

# Export and launch local server on port 8080
ExportToCellbrowser(
  object = seurat_obj,
  dir = "cellbrowser_output",
  dataset.name = "PBMC_3k",
  cb.dir = "cellbrowser_html",
  port = 8080
)

# Stop the server when done
StopCellbrowser()

​
See Also

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