dmr_manhattan_plot

pylluminator.visualizations.dmr_manhattan_plot(dm: DM, contrast: str | None = None, chromosome_col='chromosome', x_col='start', y_col='p_value_adjusted', annotation_col='genes', nb_annotated_probes: int = 100, log10=True, figsize: tuple[float, float] = (10, 8), sig_threshold: float | None = 0.05, title: None | str = None, save_path: None | str = None) → None

Display a Manhattan plot of the given DM data

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 DMR dataframe. Default: p_value

  • annotation_col (str | None) – the name of a column used to write annotation on the plots. Must be a column in the Annotation data. The top 100 regions are annotated. Default: None

  • nb_annotated_probes (int) – the number of probes to annotate (if annotation_col is provided). Defaul: 100

  • sig_threshold (float | None) – Plot only DMRs below this significance threshold. Set to None to draw all DMRs. Default: 0.05

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

  • 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