scimap.hl.scimap_to_csv

Short description

Helper function to convert andata object to a csv file with the expression matrix and available metadata.

Parameters

adata : AnnData object

data_type : string, optional (The default is 'raw')
Three options are available:
1) 'raw' - The raw data will be returned.
2) 'log' - The raw data converted to log scale using np.log1p will be returned.
3) 'scaled' - If you have scaled the data using the sm.pp.rescale, that will be returned. Please note, if you have not scaled the data, whatever is within adata.X will be returned.

Returns

A single dataframe containing the expression and metadata.

Example

data = sm.hl.scimap_to_csv (adata, data_type='raw')