Export combined cell data

Exports the expression, coordinates, and annotations contained in a SpatialMap object to a CSV file.

Usage

exportCellData(
  object,
  data_layer = "Data",
  features = NULL,
  coords = "spatial",
  annotations = NULL,
  analyze = NULL,
  base_dir = NULL,
  file_names = NULL,
  ...
)

Arguments

object

A SpatialMap object

data_layer

The name of the data slot to export

features

Specific features to export. Defaults to exporting all features.

coords

The name of the coords to use

annotations

Specific annotations to export (a column name in cellMetadata). Defaults to exporting all annotations.

analyze

What to analyze (and how). The options are "regions", NULL (activeAnalysis), the name of a currently existing formal analysis, or the name of a column in object's projectMetadata (an "informal" analysis).

base_dir

The name of the base directory in which to place the exported data. Defaults to @projectName

file_names

The name(s) of the exported file(s), without .csv extension. The number of names expected is based on the analyze parameter (i.e. for a "combined" analysis, only one name is expected). Defaults to Region IDs when analyze = NULL and activeAnalysis = "regions", but a named character vector can be used to define custom file names (names correspond to region IDs, values to file names).

...

Arguments passed to write.csv

Value

The output path(s) of the saved file(s)

Details

Further details and examples are available at vignette("Tutorial_Exporting_Data").

See also

Other exporting functions: exportAnnotations(), exportCoords(), exportData(), exportMetadata(), exportPathDefault()