analyze_replicates

pylluminator.visualizations.analyze_replicates(samples: Samples, sample_id_column: str, replicate_names: list[str] = None, return_df=False, xlim: None | tuple[float, float] = None, save_path: str = None, figsize=(10, 5), **kwargs) → DataFrame | None

Analyze the beta values standard deviation of the technical replicates to check for batch effect or quality issues.

Parameters:

  • samples (Samples) – samples with beta values already calculated

  • sample_id_column (str) – the name of the column in the sample sheet that contains the sample ids, used to identify the replicates

  • replicate_names (list[str] | None) – list of the replicate names to analyze. If None, analyze all samples. Default: None

  • return_df (bool) – if True, return the dataframe used to plot the graph. Default: False

  • xlim (tuple[float, float] | None) – set the x-axis limits. Default: None

  • save_path (str | None) – if set, save the graph to save_path. Default: None

Returns:

the dataframe with beta values standard deviation per replicate, or None if return_df is False

Return type:

pandas.DataFrame | None