FACSPy.dt.CofactorTable

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FACSPy.dt.CofactorTable#

class FACSPy.dt.CofactorTable(file='', cofactors=None, from_fcs=False)#

CofactorTable class to represent and unify cytometry cofactor representations. The structure has to be at least two columns: fcs_colname with the antigen names (e.g. CD3) and cofactors with the corresponding cofactors. If the table is supposed to be constructed from the read-in files directly, set the flag from_fcs to True.

Parameters:

  • file (str) – The path or filename pointing to the table. Can be .txt, .csv.

  • cofactors (Optional[DataFrame]) – Optional. If the dataframe has been assembled with pandas, supply this metadata dataframe.

  • from_fcs (bool) – If True, returns an empty CofactorTable object which will be filled during cofactor_calculation by fp.calculate_cofactors().

Return type:

The dataset object of CofactorTable

Examples

>>> import FACSPy as fp
>>> import pandas as pd

>>> cof_table = fp.dt.CofactorTable("cofactors.csv") # creates table from the local file `cofactors.csv`
>>> cof_table
CofactorTable(12 channels, loaded as provided file)

>>> cof_table_frame = pd.DataFrame(
...     data = {
...         "fcs_colname": ["CD3", "CD4", "CD5"],
...         "cofactors" : [200, 400, 200],
...     },
...     index = list(range(3))
... )
>>> cof_table = fp.dt.CofactorTable(cofactors = cof_table_frame) # creates table from a pd.DataFrame
>>> cof_table
CofactorTable(3 channels, loaded as provided dataframe)

Notes

See further usage examples in the following tutorials: The CofactorTable object

Methods

get_cofactor(channel_name)

returns cofactor of a given channel

rename_channel(current_name, new_name)

select_channels(channels)

selects channels and subsets dataframe

set_cofactor(channel_name, cofactor)

sets cofactor of a given channel

set_cofactors([cofactors, cytof])

sets cofactors.

set_columns(columns)

converts a column to fcs_colname column

to_df()

returns the dataframe of the object

write([output_directory])

writes the underlying table to disk.
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