scimapToCsv

scimapToCsv

scimapToCsv(
    data,
    layer="raw",
    outputDir=None,
    fileName=None,
    cellId="CellID",
    verbose=True,
    sdataTable=None,
)

Export expression and metadata as one flat table.

Produces one row per cell: a cell id, one column per marker, then every obs column. That is the shape most non-Python tools expect.

Parameters:

Name	Type	Description	Default
data	(AnnData | SpatialData | str, required)	The cell table. An AnnData, a path to an .h5ad file, a SpatialData object, or a path to a .zarr SpatialData store.	required
layer	str	Which matrix to export. 'raw' uses .raw.X, None uses .X, any other string names a key in .layers.	'raw'
outputDir	str	Directory to write the CSV into. With None nothing is written and the DataFrame is only returned.	None
fileName	str	Name of the CSV. Defaults to 'scimap_export.csv'.	None
cellId	str	Name of the first column, holding obs_names.	'CellID'
verbose	bool	Print the path written.	True
sdataTable	str	Which SpatialData table to read.	None

Returns:

Name	Type	Description
result	DataFrame	The flattened table, always returned whether or not outputDir was given.

Raises:

Type	Description
ValueError	When layer='raw' and the object has no .raw.

Example

sp.pp.scimapToCsv(adata, outputDir="results", fileName="analysis.csv")

# Export the rescaled values rather than the raw ones.
table = sp.pp.scimapToCsv(adata, layer=None)