cytonormpy._dataset.DataHandlerFCS

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cytonormpy._dataset.DataHandlerFCS#

class cytonormpy._dataset.DataHandlerFCS(metadata, input_directory=None, channels='markers', reference_column='reference', reference_value='ref', batch_column='batch', sample_identifier_column='file_name', n_cells_reference=None, transformer=None, truncate_max_range=True, output_directory=None, prefix='Norm')#

Class to intermediately represent the data, read and write outputs and handle intermediate steps.

Parameters:

  • metadata (Union[DataFrame, PathLike]) – A table containing the file names, the batch and the reference information. Expects the columns file_name, batch and reference where reference must contain ref for reference samples and other for non-reference samples. Can be provided as a DataFrame or a path.

  • input_directory (Optional[PathLike]) – Path specifying the input directory in which the .fcs files are stored. If left None, the current working directory is assumed.

  • channels (Union[list[str], str, Literal['all', 'markers']]) – Can be a list of detectors (e.g. BV421-A), a single channel or ‘all’ or ‘markers’. If markers, channels containing ‘FSC’, ‘SSC’, ‘Time’, ‘AF’ and CyTOF technicals will be excluded.

  • reference_column (str) – The column in the metadata that specifies whether a sample is used for reference and is therefore present in all batches. Defaults to ‘reference’.

  • reference_value (str) – Specifies the value that is considered a reference. Defaults to ‘ref’.

  • batch_column (str) – The column in the metadata that specifies the batch. Defaults to ‘batch’.

  • sample_identifier_column (str) – Specifies the column in the metadata that is unique to the samples. Defaults to ‘file_name’.

  • output_directory (Optional[PathLike]) – Path specifying the output directory in which the .fcs files are saved to. If left None, the current input directory is assumed.

  • prefix (str) – The prefix that are prepended to the file names of the normalized fcs files.

Return type:

None

Attributes

cytof_technicals

flow_technicals

spectral_flow_technicals

metadata

n_cells_reference

Methods

add_file(file_name, batch)

append_cytof_technicals(value)

append_flow_technicals(value)

append_spectral_flow_technicals(value)

get_corresponding_ref_dataframe(file_name)

Returns the data of the corresponding reference for the indicated file name.

get_dataframe(file_name)

Returns a dataframe for the indicated file name.

get_ref_data_df([markers])

Returns the reference data frame.

get_ref_data_df_subsampled(n[, markers])

Returns the reference data frame, subsampled to n events.

write(file_name, data[, output_dir])

Writes the data to the hard drive as an .fcs file.
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