cellink.pl.locus

cellink.pl.locus(locus_df, gene_df=None, pval_col='pval', position_col='pos', label_column=None, significance_threshold=None, highlight_color='#D62728', point_size=20, figsize=(10, 5), labelsize=10, titlesize=14, title=None, gene_color='#1f77b4', gene_style='box', show_genes=True, show=None, save=None, dpi=300, ax=None)

Generate a locus plot with SNP p-values and optional gene annotations.

Parameters:

• locus_df (pandas.DataFrame) – DataFrame containing SNP positions and p-values.

• gene_df (pandas.DataFrame, optional) – DataFrame of gene annotations with columns: “start”, “end”, “gene”, and optionally “strand”.

• pval_col (str, default "pval") – Column name in locus_df for p-values.

• position_col (str, default "pos") – Column name in locus_df for genomic positions.

• label_column (str or None, optional) – Column in locus_df used to label significant SNPs.

• significance_threshold (float, optional) – Threshold below which SNPs are highlighted and optionally labeled.

• highlight_color (str, default "#D62728") – Color used to highlight significant SNPs.

• point_size (int, default 20) – Size of scatter plot points.

• figsize (tuple, default (10, 5)) – Size of the figure (width, height) in inches.

• labelsize (int, default 10) – Font size for axis and annotation labels.

• titlesize (int, default 14) – Font size for the plot title.

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

• gene_color (str, default "#1f77b4") – Color used for gene annotations.

• gene_style ({'box', 'bracket'}, default "box") – Style used for gene annotations. “box” draws rectangles, “bracket” draws lines with caps.

• show_genes (bool, default True) – Whether to include gene annotations beneath the plot.

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

• save (str or bool or None, optional) – If a string, saves the plot to the specified file path. If True, saves as “locus_plot.png”.

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

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

Return type:

Figure

Returns:

matplotlib.figure.Figure The resulting locus plot figure.