Export coordinates

Exports the coordinates/embeddings contained in a SpatialMap object to a CSV file.

Usage

exportCoords(
  object,
  coords = "spatial",
  analyze = "regions",
  base_dir = NULL,
  file_names = NULL,
  ...
)

Arguments

object

A SpatialMap object

coords

The name of the coords to use

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

Details

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

Note

In the current implementation, spatial coordinates cannot be exported for combined analyses. It is recommended to export spatial coordinates by regions, then to concatenate the files.

See also

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