cellink.pl.manhattan

cellink.pl.manhattan(pvals_df, pval_col='pv_adj', chromosome_col='chrom', position_col='pos', point_size=10, significance_threshold=None, label_column=None, figsize=None, labelsize=None, titlesize=None, title=None, palette_mode='alternating', palette_alternating_colors=['#E24E42', '#008F95'], significant_hit_color='#D62728', palette=None, show=None, save=None, dpi=300, ax=None)

Generate a Manhattan plot for genome-wide association p-values.

Parameters:

• pvals_df (pandas.DataFrame) – DataFrame containing p-values and variant genomic positions.

• pval_col (str, default "pv_adj") – Column in pvals_df with p-values.

• chromosome_col (str) – Column name for chromosome numbers (can be numeric or ‘X’, ‘Y’).

• position_col (str) – Column name for base-pair positions.

• point_size (int) – Size of points.

• significance_threshold (float, default 5e-8) – Threshold for highlighting significant hits.

• label_column (str or None) – Column to use for labeling significant points. Labels are shown above points.

• figsize (tuple, optional) – Size of the figure. Defaults to matplotlib’s figure.figsize.

• labelsize (int, optional) – Font size for axis labels. Defaults to matplotlib’s axes.labelsize.

• titlesize (int, optional) – Font size for the title. Defaults to matplotlib’s axes.titlesize.

• title (str, optional) – Title for the plot.

• palette_mode ({'alternating', None}, default 'alternating') – Color mode for chromosomes if no palette is specified.

• palette_alternating_colors (list or np.ndarray, default ['#E24E42', '#008F95']) – List of two colors used to alternate chromosome coloring.

• significant_hit_color (str, default "#D62728") – Color for highlighting significant hits.

• palette (str or None) – Seaborn color palette name. Overrides palette_mode if provided.

• show (bool or None) – Whether to display the plot. If None, shows the plot only when ax is not provided.

• save (str or bool or None) – File path to save the plot. If True, saves as “manhattan.png”.

• dpi (int, default 300) – Resolution (dots per inch) of the saved figure.

• ax (matplotlib.axes.Axes or None) – Optional matplotlib Axes object to plot into.

Return type:

Figure

Returns:

matplotlib.figure.Figure The resulting Manhattan plot figure.

Raises:

ValueError – If both palette and palette_mode are specified simultaneously.