scimap_to_csv
Short Description
sm.hl.scimap_to_csv
: Helper function that allows users to save the contents of the scimap
object as a csv file.
Please not that anything that it only saves elements that are within adata.X or adata.raw.X
and adata.obs
.
Function
scimap_to_csv(adata, data_type='raw', output_dir=None, file_name=None, CellID='CellID')
Parameters:
Name | Type | Description | Default |
---|---|---|---|
adata |
AnnData object loaded into memory or path to AnnData object. |
required | |
data_type |
string
|
Three options are available: |
'raw'
|
output_dir |
string
|
Path to output directory. |
None
|
file_name |
string
|
Name the output csv file. Use in combination with |
None
|
CellID |
string
|
Name of the column which contains the CellID. Default is |
'CellID'
|
Returns:
Name | Type | Description |
---|---|---|
merged |
DataFrame
|
A single dataframe containing the expression and metadata will be returned. |
1 |
|
Source code in scimap/helpers/_scimap_to_csv.py
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