scimap_to_csv

Short Description

sm.hl.scimap_to_csv: This utility function facilitates exporting the contents of a scimap object (AnnData) to a CSV file, combining gene expression data from adata.X or adata.raw.X with cell metadata from adata.obs. It provides a streamlined way to save and share data for further analysis or documentation. Note that the export focuses on the expression matrix and associated cell annotations. It does not export information saved in adata.uns

Function

scimap_to_csv(adata, layer='raw', output_dir=None, file_name=None, CellID='CellID', verbose=True)

Parameters:

Name	Type	Description	Default
adata	AnnData	The annotated data matrix to export.	required
layer	str	Specifies the layer to export: - 'raw': Exports the raw data. - 'log': Exports the data after applying a log transformation with np.log1p. - 'None': Exports the data in adata.X	'raw'
output_dir	str	The directory where the CSV file will be saved. If not specified, the file is saved in the current working directory.	None
file_name	str	The name of the output CSV file. If not provided, a default name scimap_to_csv_file.csv is used.	None
CellID	str	The column name in the output CSV file that will contain the Cell IDs.	'CellID'
verbose	bool	If True, prints messages about the export process.	True

Returns:

Name	Type	Description
DataFrame	csv	The function does not return a value but saves the specified data to a CSV file in the designated directory.

Example

    # Export raw data to CSV
    sm.hl.scimap_to_csv(adata, layer='raw', output_dir='/path/to/save', file_name='raw_data.csv')

    # Export log-transformed data to CSV, with a custom CellID column name
    sm.hl.scimap_to_csv(adata, layer='log', output_dir='/path/to/save', file_name='log_data.csv', CellID='UniqueCellID')

    # Export scaled data to Cobject
    data = sm.hl.scimap_to_csv(adata, layer='scaled')

Source code in scimap/helpers/scimap_to_csv.py

def scimap_to_csv (adata, 
                   layer='raw', 
                   output_dir=None, 
                   file_name=None, 
                   CellID='CellID',
                   verbose=True):
    """
Parameters:
        adata (anndata.AnnData):  
            The annotated data matrix to export.

        layer (str, optional):  
            Specifies the layer to export:
            - 'raw': Exports the raw data.
            - 'log': Exports the data after applying a log transformation with `np.log1p`.
            - 'None': Exports the data  in `adata.X`

        output_dir (str, optional):  
            The directory where the CSV file will be saved. If not specified, the file is saved in the current working directory.

        file_name (str, optional):  
            The name of the output CSV file. If not provided, a default name `scimap_to_csv_file.csv` is used.

        CellID (str, optional):  
            The column name in the output CSV file that will contain the Cell IDs. 

        verbose (bool, optional):  
            If True, prints messages about the export process.

Returns:
        DataFrame (csv):  
            The function does not return a value but saves the specified data to a CSV file in the designated directory.

Example:
    ```python

        # Export raw data to CSV
        sm.hl.scimap_to_csv(adata, layer='raw', output_dir='/path/to/save', file_name='raw_data.csv')

        # Export log-transformed data to CSV, with a custom CellID column name
        sm.hl.scimap_to_csv(adata, layer='log', output_dir='/path/to/save', file_name='log_data.csv', CellID='UniqueCellID')

        # Export scaled data to Cobject
        data = sm.hl.scimap_to_csv(adata, layer='scaled')

    ```
    """

    # Load the andata object    
    if isinstance(adata, str):
        if file_name is None:
            imid = str(adata.rsplit('/', 1)[-1])
        else: 
            imid = str(file_name)
        adata = ad.read(adata)
    else:
        if file_name is None:
            imid = "scimap_to_csv_file.csv"
        else: 
            imid = str(file_name)
        adata = adata


    # Expression matrix
    if layer == 'raw':
        data = pd.DataFrame(adata.raw.X, index=adata.obs.index, columns=adata.var.index)
    elif layer is None:
        data = pd.DataFrame(adata.X, index=adata.obs.index, columns=adata.var.index)
    else:
        data = pd.DataFrame(adata.layers[layer], index=adata.obs.index, columns=adata.var.index)


# =============================================================================
#     # Expression matrix
#     if data_type == 'raw':
#         data = pd.DataFrame(adata.raw.X, index=adata.obs.index, columns=adata.var.index)
#     if data_type == 'log':
#         data = pd.DataFrame(np.log1p(adata.raw.X), index=adata.obs.index, columns=adata.var.index)
#     if data_type == 'scaled':
#         data = pd.DataFrame(adata.X, index=adata.obs.index, columns=adata.var.index)
# =============================================================================

    # Metadata
    meta = pd.DataFrame(adata.obs)

    # Merge the two dataframes
    merged = pd.concat([data, meta], axis=1, sort=False)

    # Add a column to save cell-id
    #merged['CellID'] = merged.index
    # make cellID the first column
    if CellID in merged.columns:
        first_column = merged.pop(CellID)
        merged.insert(0, CellID, first_column)
    else:
        merged['CellID'] = merged.index
        first_column = merged.pop(CellID)
        merged.insert(0, CellID, first_column)

    # reset index
    merged = merged.reset_index(drop=True)

    # Save data if requested
    if output_dir is not None:
        output_dir = pathlib.Path(output_dir)
        output_dir.mkdir(exist_ok=True, parents=True)
        merged.to_csv(output_dir / f'{imid}.csv', index=False)
    else:    
        # Return data
        return merged