manhattan_plot_dmr

pylluminator.visualizations.manhattan_plot_dmr(dm: DM, contrast: str, chromosome_col='chromosome', x_col='start', y_col='p_value', annotation_col='genes', log10=True, draw_significance=True, figsize: tuple[float, float] = (10, 8), medium_threshold: float | None = None, high_threshold: float | None = None, title: None | str = None, save_path: None | str = None) → None

Display a Manhattan plot of the given DMR data, designed to work with the dataframe returned by get_dmrs()

Parameters:

  • dm (pylluminator.DM) – DM object with computed DMRs

  • contrast (str) – name of the contrast to use.

  • chromosome_col (str) – the name of the chromosome column in the dmr dataframe. Default: chromosome

  • x_col (str) – name of the column to use for X axis, start position of the probe/bin. Default: start

  • y_col (str) – the name of the value column in the data_to_plot dataframe. Default: p_value

  • annotation_col (str | None) – the name of a column used to write annotation on the plots for data that is above the significant threshold. Must be a column in the Annotation data. Default: None

  • medium_threshold (float | None) – set the threshold used for displaying annotation (and significance line if raw_significance is True). If None, takes the value of the 100th probe. Default: None

  • high_threshold (float | None) – set the threshold for the higher significance line (drawn if draw_significance is True). If None, takes the value of the 20th probe. Default: None

  • log10 (bool) – apply -log10 on the value column. Default: True

  • draw_significance (bool) – draw p-value significance lines (at 1e-05 and 5e-08). Default: False

  • figsize (tuple) – size of the figure. Default: (10, 8)

  • title (str | None) – custom title for the plot. Default: None

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

Returns:

nothing