tdm.preprocess.ki67.transform_ki67

tdm.preprocess.ki67.transform_ki67(single_cell_df: DataFrame, typical_noise: float = 0.5, ki67_col: str = 'ki67', cell_type_col: str = 'cell_type')

Return a single-cell dataframe with standardized Ki67 values above noise, the transformed distributions should have similar shapes.

Parameters:

• single_cell_df (pd.DataFrame) – dataframe with row per cell, columns for cell type and Ki67 values.

• typical_noise (float, optional) – magnitude of typical noise in the data. See example plot for finding the typical noise

:param in tutorial 01.: :param ki67_col: name of the column with Ki67 values. :type ki67_col: str :param cell_type_col: name of the column with cell types. :type cell_type_col: str

Note

The transformed values should have similar distributions accross different cell types. To plot the transformed values:

from tdm.preprocess.ki67 import transform_ki67, plot_marker_distributions

transformed_ki67_single_cell_df = transform_ki67(single_cell_df)
plot_marker_distributions(transformed_ki67_single_cell_df, ki67_col)

Returns:

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Return type:

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