{
  "param_groups": {
    "highlight": [
      "highlight",
      "highlight_chrpos",
      "highlight_color",
      "highlight_anno_kwargs",
      "highlight_anno_args",
      "highlight_lim",
      "highlight_lim_mode",
      "highlight_windowkb"
    ],
    "ld": [
      "anno_cell",
      "anno_cell_fmt",
      "anno_cell_kwargs",
      "cbar_bbox_to_anchor",
      "cbar_borderpad",
      "cbar_downward_offset",
      "cbar_equal_aspect",
      "cbar_font_family",
      "cbar_fontsize",
      "cbar_h_scale",
      "cbar_scale",
      "cbar_title",
      "cbar_w_scale",
      "ld_block",
      "ld_block_anno",
      "ld_block_anno_kwargs",
      "ld_block_anno_max_rows",
      "ld_block_anno_set",
      "ld_block_grid",
      "ld_block_grid_kwargs",
      "ld_fmt",
      "ld_if_add_T",
      "ld_if_square",
      "ld_link",
      "ld_link_alpha_scale",
      "ld_link_color",
      "ld_link_linewidth",
      "ld_link_sig_level",
      "ld_link_thr",
      "ld_map_kwargs",
      "ld_map_path",
      "ld_map_rename_dic",
      "ld_path",
      "show_ld_score",
      "tabix",
      "taf",
      "vcf_chr_dict",
      "vcf_path"
    ],
    "rr": [
      "region_recombination",
      "rr_chr_dict",
      "rr_header_dict",
      "rr_lim",
      "rr_path",
      "rr_ylabel"
    ],
    "region_panel": [
      "gtf_chr_dict",
      "gtf_gene_name",
      "gtf_path",
      "region",
      "region_anno_bbox_args",
      "region_anno_bbox_kwargs",
      "region_flank_factor",
      "region_grid",
      "region_grid_line",
      "region_hspace",
      "region_ld_colors",
      "region_ld_colors_m",
      "region_ld_legend",
      "region_ld_threshold",
      "region_lead_grid",
      "region_lead_grid_line",
      "region_legend_marker",
      "region_marker_shapes",
      "region_protein_coding",
      "region_ref",
      "region_ref_alias",
      "region_ref_second",
      "region_step",
      "region_title",
      "region_title_args",
      "region_title_kwargs",
      "track_exon_ratio",
      "track_font_family",
      "track_fontsize_ratio",
      "track_n",
      "track_n_offset",
      "track_text_offset"
    ],
    "qq_panel": [
      "gc",
      "qq_line_color",
      "qq_scatter_args",
      "qq_scatter_kwargs",
      "qq_xlabels",
      "qq_xlim",
      "qtitle",
      "qtitle_pad",
      "stratified"
    ],
    "mqq_layout": [
      "mqqratio",
      "mtitle",
      "mtitle_pad"
    ],
    "brisbane": [
      "bwindowsizekb",
      "density_color",
      "density_palette",
      "density_range",
      "density_threshold",
      "density_tpalette",
      "density_trange"
    ],
    "qq_misc": [
      "include_chrXYMT",
      "expected_min_mlog10p"
    ],
    "pinpoint": [
      "pinpoint",
      "pinpoint_color"
    ],
    "jagged_axis": [
      "jagged",
      "jagged_len",
      "jagged_wid"
    ],
    "maf_stratify": [
      "maf_bins",
      "maf_bin_colors"
    ],
    "panel_layout": [
      "height_ratios",
      "hspace",
      "subplot_height",
      "titles",
      "title_pos",
      "align_xaxis",
      "variant_positions",
      "variant_line_kwargs"
    ],
    "track_panel": [
      "file_format",
      "chr_dict",
      "name_column",
      "feature_type",
      "min_track_height",
      "figsize"
    ],
    "arc_panel": [
      "arc_height",
      "max_arcs",
      "score_col",
      "score_threshold",
      "color_by_score"
    ],
    "ag_panel": [
      "filled",
      "ylabel_template",
      "cmap",
      "vmin",
      "vmax",
      "filter_threshold"
    ],
    "chromatin_panel": [
      "region_chromatin_labels",
      "xlim_i"
    ]
  },
  "args": {
    "_chrom_df_for_i": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Internal MQQ helper; not for user calls.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "_get_region_lead": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Internal regional helper; not for user calls.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "_if_quick_qc": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Internal QC flag; not for user calls.",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "_invert": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Internal axis helper; not for user calls.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "_posdiccul": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Internal position dict; not for user calls.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "add_b": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Add Manhattan panel below",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "additional_line": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Additional reference lines",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "additional_line_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Colors for additional lines",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "adjust_text_kwargs": {
      "plots": [
        "compare_effect"
      ],
      "desc": "AdjustText kwargs for annotations",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "adjust_text_kwargs_l": {
      "plots": [
        "compare_effect"
      ],
      "desc": "AdjustText kwargs (left side)",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "adjust_text_kwargs_r": {
      "plots": [
        "compare_effect"
      ],
      "desc": "AdjustText kwargs (right side)",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "allele_match": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Align alleles before comparison",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "alpha": {
      "plots": [
        "plot_arc",
        "plot_gwheatmap"
      ],
      "desc": "Alpha for markers",
      "default": 0.5,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "arc_panel"
    },
    "anno": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_stacked_mqq",
        "plot_phenogram"
      ],
      "desc": "Annotation source or column (e.g., 'GENENAME', True, or column name)",
      "default": null,
      "ctx_defaults": {
        "compare_effect": false
      },
      "add_to_docstring": false
    },
    "anno_adjust": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Enable annotation position adjustment",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_alias": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region",
        "plot_stacked_mqq",
        "plot_phenogram"
      ],
      "desc": "Mapping from SNPID to custom annotation label",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_d": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Per-annotation positioning options (e.g., left/right)",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_diff": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Annotation difference threshold",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_fixed_arm_length": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Fixed arm length for annotations",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_fontsize": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_stacked_mqq"
      ],
      "desc": "Font size for annotation text",
      "default": 9,
      "ctx_defaults": {
        "plot_region:r": 9,
        "plot_mqq": 9
      },
      "add_to_docstring": false
    },
    "anno_gtf_path": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq",
        "plot_phenogram"
      ],
      "desc": "Custom GTF path for annotations",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_height": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Height for annotations",
      "default": 1,
      "ctx_defaults": {
        "plot_region:r": 1,
        "plot_mqq": 1
      },
      "add_to_docstring": false
    },
    "anno_het": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Enable heterogeneity annotation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_kwargs": {
      "plots": [
        "compare_effect",
        "plot_mqq",
        "plot_region",
        "plot_snp_density",
        "plot_miami2",
        "plot_manhattan",
        "plot_stacked_mqq",
        "plot_phenogram"
      ],
      "desc": "Default styling kwargs for annotations",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_kwargs_single": {
      "plots": [
        "compare_effect",
        "plot_mqq",
        "plot_phenogram",
        "plot_region",
        "plot_snp_density",
        "plot_miami2",
        "plot_manhattan",
        "plot_stacked_mqq"
      ],
      "desc": "Per-SNP styling kwargs for annotations",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_max_iter": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Maximum iterations for text repulsion algorithm",
      "default": 100,
      "ctx_defaults": {
        "plot_region:r": 100,
        "plot_mqq": 100
      },
      "add_to_docstring": false
    },
    "anno_max_rows": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_region",
        "plot_region:r",
        "plot_snp_density",
        "plot_stacked_mqq"
      ],
      "desc": "Maximum number of annotation rows to display. If more variants are provided, they will be sorted by p-value or -log10(p-value) and only the top ones will be shown.",
      "default": 40,
      "ctx_defaults": {
        "plot_phenogram": 200
      },
      "add_to_docstring": true
    },
    "anno_x_pad": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Phenogram extra horizontal gap between chromosome and annotation text (data coords)",
      "default": 0.18,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_group": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Column name to merge multiple phenogram leads into one label",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_shape": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Column name for phenogram marker shape; unique values auto-mapped to marker_shapes pool",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_color": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Column name for phenogram marker color; unique values auto-mapped to marker_colors pool",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "use_lead_extraction": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "If True, extract lead variants via _get_sig(); if False, use every input row",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "include_sex_chr": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "If True, include chrX and chrY after autosomes in phenogram",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "only_anno_chr": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "If True, plot only chromosomes containing phenogram lead or annotation rows",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_shapes": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Pool of matplotlib marker codes for auto phenogram shape mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_colors": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Pool of colors for auto phenogram color mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_min": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Minimum -log10(P) for annotation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_min1": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Min threshold for series 1 annotation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_min2": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Min threshold for series 2 annotation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_set": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:b",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_region",
        "plot_snp_density:b",
        "plot_snp_density",
        "plot_stacked_mqq",
        "plot_phenogram"
      ],
      "desc": "Set of variant IDs to annotate",
      "default": [],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_source": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq",
        "plot_phenogram"
      ],
      "desc": "Annotation source backend (e.g., 'ensembl', 'refseq')",
      "default": "ensembl",
      "ctx_defaults": {
        "plot_region:r": "ensembl",
        "plot_mqq": "ensembl"
      },
      "add_to_docstring": false
    },
    "anno_style": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Annotation style ('right', 'tight', 'expand')",
      "default": "right",
      "ctx_defaults": {
        "plot_region:r": "right",
        "plot_mqq": "right"
      },
      "add_to_docstring": false
    },
    "anno_x": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Annotation x threshold",
      "default": 0.01,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_xshift": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "X-axis shift applied to annotations",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_y": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Annotation y threshold",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "arm_offset": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Offset for annotation arms",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "arm_scale": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Scaling factor for arm length",
      "default": 1,
      "ctx_defaults": {
        "plot_region:r": 1,
        "plot_mqq": 1
      },
      "add_to_docstring": false
    },
    "arm_scale_d": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Per-annotation arm scaling dict",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "arrow_kwargs": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_phenogram",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Arrow styling kwargs for annotations",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "asize": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Annotation size",
      "default": 10,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "associations": {
      "plots": [],
      "desc": "",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "beta": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Effect size column",
      "default": "BETA",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "beta_range": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Beta range for power computation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "build": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Genome build (e.g., '19'/'38') for annotation/coordinate resources",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "bwindowsizekb": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Window size in kilobases for density computation",
      "default": 100,
      "ctx_defaults": {
        "plot_snp_density:b": 100
      },
      "add_to_docstring": false
    },
    "cbar_bbox_to_anchor": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colorbar bbox_to_anchor",
      "default": [
        0,
        0,
        1,
        1
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_borderpad": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colorbar border padding",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_downward_offset": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colorbar downward offset",
      "default": 1.3,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_equal_aspect": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Equal aspect for colorbar",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_font_family": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colorbar font family",
      "default": "Arial",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_fontsize": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Colorbar font size",
      "default": 12,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_h_scale": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colorbar height scale",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_scale": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Scale colorbar",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_title": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Title text for the LD r\u00b2 colorbar inset.",
      "default": "LD $\\mathregular{r^2}$ with variant",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Shown when region_ld_legend=True; LaTeX r\u00b2 supported in default."
      }
    },
    "cbar_w_scale": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colorbar width scale",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "check": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Enable input QC and normalization",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "chr_dict": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_track"
      ],
      "desc": "Chromosome number/name mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "track_panel"
    },
    "chrom": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Chromosome column used to position variants and x-axis layout",
      "default": "CHR",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "chr_width": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Phenogram chromosome width in data coordinates",
      "default": 0.35,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "chr_x": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Phenogram chromosome left x boundary in data coordinates",
      "default": 0.0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "chrpad": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Chromosome padding proportion",
      "default": 0.03,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cis_windowsizekb": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Window size (kb) for cis-regulatory heatmap rows.",
      "default": 100,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_gwheatmap": "Cis-window half-width (kb) for rows in the GWAS heatmap."
      }
    },
    "cmap": {
      "plots": [
        "plot_ag_contact",
        "plot_ag_overlay",
        "plot_ag_sashimi",
        "plot_ag_tracks",
        "plot_associations",
        "plot_rg",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Colormap selection",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "ag_panel"
    },
    "cmap_rg": {
      "plots": [],
      "desc": "Colormap for RG heatmap",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "colorbar_kwargs": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Colorbar kwargs",
      "default": {
        "shrink": 0.82
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "colors": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq",
        "plot_region:r",
        "plot_snp_density:b"
      ],
      "desc": "Color palette or list",
      "default": [
        "#597FBD",
        "#74BAD3"
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "ag_panel"
    },
    "corrections": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Multiple testing corrections",
      "default": [
        "non",
        "fdr",
        "bon"
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cs": {
      "plots": [
        "plot_pipcs"
      ],
      "desc": "Column name for credible-set index.",
      "default": "CREDIBLE_SET_INDEX",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_pipcs": "Credible-set index column."
      }
    },
    "cs_category": {
      "plots": [
        "plot_pipcs"
      ],
      "desc": "Column name for credible-set category label.",
      "default": "CS_CATEGORY",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cut": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Cap variant -log10(P) display above this value (squashes extreme peaks for layout).",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cut_line_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Color for shrink line",
      "default": "#ebebeb",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cut_log": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Use log scale for cut line",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cutfactor": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Factor for shrink line",
      "default": 10,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "daf": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Column name for discovery allele frequency.",
      "default": "DAF",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_daf": "Discovery allele frequency column."
      }
    },
    "density_color": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Density palette or boolean to control density track colors",
      "default": false,
      "ctx_defaults": {
        "plot_snp_density:b": false
      },
      "add_to_docstring": false,
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "brisbane"
    },
    "density_palette": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Density palette",
      "default": "Reds",
      "ctx_defaults": {
        "plot_snp_density:b": "Reds"
      },
      "add_to_docstring": false
    },
    "density_range": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Density value range",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "density_threshold": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Threshold for density highlighting",
      "default": 5,
      "ctx_defaults": {
        "plot_snp_density:b": 5
      },
      "add_to_docstring": false
    },
    "density_tpalette": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Palette for threshold coloring",
      "default": "Blues",
      "ctx_defaults": {
        "plot_snp_density:b": "Blues"
      },
      "add_to_docstring": false
    },
    "density_trange": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_snp_density:b"
      ],
      "desc": "Threshold range",
      "default": [
        0,
        10
      ],
      "ctx_defaults": {
        "plot_snp_density:b": [
          0,
          10
        ]
      },
      "add_to_docstring": false
    },
    "dpi": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Figure DPI",
      "default": 200,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "drop": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Drop variants by condition",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "drop_chr_start": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Drop chromosome start",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ea": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Effect allele column",
      "default": "EA",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "eaf": {
      "plots": [
        "plot_daf",
        "plot_effect",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Effect allele frequency column",
      "default": "EAF",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_daf": "Effect allele frequency column for DAF comparison plot."
      }
    },
    "eaf_kwargs": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Styling kwargs for EAF panel",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "eaf_label": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Label for EAF panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "eaf_panel": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Toggle EAF panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "edgecolor": {
      "plots": [],
      "desc": "Marker edge color",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "effect_label": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Label for effect size panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "equal_aspect": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Keep equal aspect ratio",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "err_kwargs": {
      "plots": [
        "compare_effect",
        "plot_effect"
      ],
      "desc": "Errorbar styling kwargs",
      "default": {},
      "ctx_defaults": {
        "plot_effect": {
          "ecolor": "#cccccc",
          "linewidth": 0,
          "zorder": 90,
          "elinewidth": 1
        },
        "compare_effect": {
          "ecolor": "#cccccc",
          "elinewidth": 1
        }
      },
      "add_to_docstring": false
    },
    "expected_min_mlog10p": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Expected minimum -log10(P) adjustment",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fdr_method": {
      "plots": [
        "plot_rg"
      ],
      "desc": "FDR correction method",
      "default": "bh",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fig_kwargs": {
      "plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_rg",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Figure kwargs for plot",
      "default": null,
      "ctx_defaults": {
        "plot_mqq:mqq": {
          "figsize": [
            15,
            5
          ],
          "dpi": 200
        },
        "plot_mqq:qqm": {
          "figsize": [
            15,
            5
          ],
          "dpi": 200
        },
        "plot_mqq:m": {
          "figsize": [
            15,
            5
          ],
          "dpi": 200
        },
        "plot_manhattan": {
          "figsize": [
            15,
            5
          ],
          "dpi": 200
        },
        "plot_snp_density": {
          "figsize": [
            15,
            5
          ],
          "dpi": 200
        },
        "plot_miami2": {
          "figsize": [
            15,
            10
          ],
          "dpi": 200
        },
        "plot_qq": {
          "figsize": [
            5,
            5
          ],
          "dpi": 200
        },
        "plot_mqq:qq": {
          "figsize": [
            5,
            5
          ],
          "dpi": 200
        },
        "plot_region": {
          "figsize": [
            15,
            15
          ],
          "dpi": 200
        },
        "plot_mqq:r": {
          "figsize": [
            15,
            15
          ],
          "dpi": 200
        },
        "plot_phenogram": {
          "figsize": [
            15,
            15
          ],
          "dpi": 200
        },
        "plot_stacked_mqq": {
          "dpi": 200
        }
      },
      "add_to_docstring": false
    },
    "figargs": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Figure kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "figax": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_snp_density:b"
      ],
      "desc": "Existing figure/axes tuple to draw on",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "font_family": {
      "plots": [
        "plot_associations",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Font family, e.g., 'Arial', for consistent styling",
      "default": "Arial",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "font_kwargs": {
      "plots": [
        "compare_effect",
        "plot_daf",
        "plot_effect"
      ],
      "desc": "Font configuration kwargs",
      "default": {
        "fontsize": 9
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fontfamily": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Font family alias",
      "default": "Arial",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fontsize": {
      "plots": [
        "plot_associations",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_rg",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Font size for ticks, labels, etc.",
      "default": 12,
      "ctx_defaults": {
        "plot_mqq:mqq": 10,
        "plot_mqq:qqm": 10
      },
      "add_to_docstring": false
    },
    "full_cell": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Fill full cell when significant",
      "default": [
        "fdr",
        0.05
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gap": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Panel gap or spacing",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gc": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Compute genomic control lambda",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "get_lead_kwargs": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Kwargs for extracting lead variants",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "grid_linecolor": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Grid line color",
      "default": "grey",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "grid_linewidth": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Grid linewidth",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "group": {
      "plots": [
        "plot_effect",
        "plot_gwheatmap"
      ],
      "desc": "Grouping column for axes",
      "default": "CIS/TRANS",
      "ctx_defaults": {
        "plot_effect": null
      },
      "add_to_docstring": false
    },
    "gtf_chr_dict": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "GTF chromosome dictionary",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gtf_gene_name": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "GTF gene name column",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gtf_path": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Gene annotation GTF for the track below the locus.",
      "default": "default",
      "ctx_defaults": {
        "plot_region:r": "default"
      },
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "'default' uses built-in annotation for build. Filter protein-coding with region_protein_coding."
      }
    },
    "height_ratios": {
      "plots": [
        "plot_gwheatmap",
        "plot_panels"
      ],
      "desc": "Panel height ratios",
      "default": null,
      "ctx_defaults": {
        "plot_gwheatmap": [
          1,
          2
        ]
      },
      "add_to_docstring": false,
      "no_plots_group": "panel_layout",
      "no_plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_gwheatmap",
        "plot_ld_block",
        "plot_lead_overlap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_pipcs",
        "plot_power",
        "plot_power:b",
        "plot_power:q",
        "plot_power_x",
        "plot_qq:qq",
        "plot_region",
        "plot_region:r",
        "plot_rg",
        "plot_sankey",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_stacked_mqq",
        "plot_trumpet",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ]
    },
    "helper_line_kwargs": {
      "plots": [
        "compare_effect",
        "plot_daf"
      ],
      "desc": "45-degree helper line styling for AF comparison",
      "default": {
        "color": "black",
        "linestyle": "-",
        "lw": 1
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight": {
      "plots": [
        "plot_manhattan",
        "plot_snp_density",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:b",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:qq",
        "plot_qq",
        "plot_qq:qq",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_stacked_mqq",
        "compare_effect"
      ],
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "highlight",
      "desc": "List of focal variants to highlight",
      "default": [],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_anno_kwargs": {
      "plots": [
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Annotation style kwargs for highlighted variants",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_chrpos": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Highlight by chromosome position flag",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_track",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Highlight color",
      "default": "#CB132D",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "track_panel"
    },
    "highlight_lim": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Custom highlight limits",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_lim_mode": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Highlight limit mode ('absolute'|'relative')",
      "default": "absolute",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_windowkb": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Highlight window size (kb)",
      "default": 500,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "histplot_kwargs": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Histogram plotting kwargs for AF distribution",
      "default": {
        "log_scale": [
          false,
          false
        ]
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "hspace": {
      "plots": [
        "plot_gwheatmap",
        "plot_panels"
      ],
      "desc": "Vertical space between panels",
      "default": 0.1,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "hue": {
      "plots": [
        "plot_effect",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Hue mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "id0": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "Identifier for miami plot pair base",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "id1": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "Identifier for series 1",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "id2": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "Identifier for series 2",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "include_all": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Include all variants for plotting",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "include_chrXYMT": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Include sex/MT chromosomes in QQ",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "qq_misc"
    },
    "insumstats": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Internal Sumstats reference; hidden from user docs.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "is_45_helper_line": {
      "plots": [
        "compare_effect",
        "plot_daf"
      ],
      "desc": "Draw 45-degree helper line",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "is_q": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Treat inputs as odds ratios",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "is_q_mc": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Monte Carlo mode for OR inputs",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "is_reg": {
      "plots": [
        "compare_effect",
        "plot_daf"
      ],
      "desc": "Enable regression line computation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "is_threshold": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Draw threshold line",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "jagged": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Enable jagged axis break markers",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "jagged_axis"
    },
    "jagged_len": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Jagged marker length",
      "default": 0.01,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "jagged_wid": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Jagged marker width",
      "default": 0.01,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "label": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Legend labels or series labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_fmt": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "LD format identifier (e.g., 'npz')",
      "default": "npz",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_if_add_T": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Add transpose when composing LD",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_if_square": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Treat LD matrix as square",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_map_kwargs": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Extra kwargs for LD map loader",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_map_path": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Path to LD map file",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_map_rename_dic": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Rename dictionary for LD map columns",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_path": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Precomputed LD matrix path (alternative to vcf_path).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "When set with ld_fmt, skips VCF LD calculation."
      }
    },
    "anno_cell": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Annotate LD block matrix cells with r\u00b2 values.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Used with ld_block=True; format via anno_cell_fmt."
      }
    },
    "anno_cell_fmt": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Format string for LD cell annotations (e.g., '{:.2f}' for 2 decimal places).",
      "default": "{:.2f}",
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "anno_cell_kwargs": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Additional keyword arguments for LD cell text annotations (e.g., {'fontsize': 10, 'weight': 'bold', 'color': 'white'}).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "ld_block_grid": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Draw grid lines on the LD matrix triangle panel.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Style via ld_block_grid_kwargs; panel requires ld_block=True."
      }
    },
    "ld_block_grid_kwargs": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Additional keyword arguments for LD block grid lines (e.g., {'color': 'gray', 'linewidth': 0.5, 'alpha': 0.5}).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "ld_block_anno": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Whether to add annotations on the left side of the LD block triangle. If True, uses 'chr:pos' format. If a string (e.g., 'SNPID', 'rsID'), uses that column for annotation text. Annotations are styled like axis ticks and labels, with right-aligned text.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Left-side variant labels on the LD triangle; True uses chr:pos, or pass a column name (SNPID, rsID)."
      }
    },
    "ld_block_anno_kwargs": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Additional keyword arguments for left-side annotations (e.g., {'fontsize': 8, 'color': 'black'}).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "ld_block_anno_set": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "List of SNPIDs to annotate. If None, annotates all variants. Variants are matched by SNPID column.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "ld_block_anno_max_rows": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Maximum number of variants to annotate. If the number of variants to annotate exceeds this limit, annotations will be skipped.",
      "default": 100,
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "ld_block": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Add rotated LD matrix (lower triangle) panel below the locus.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:b",
        "plot_mqq:qq",
        "plot_qq",
        "plot_qq:qq",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_miami2"
      ],
      "no_plots_group": "ld",
      "ctx_desc": {
        "plot_region:r": "Requires vcf_path (or ld_path) and region. Controlled with ld_block_grid/anno_* options."
      }
    },
    "ld_link": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Draw straight lines between variant pairs with LD r\u00b2 \u2265 region_ld_threshold[0].",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Draws pairs with r\u00b2 \u2265 region_ld_threshold[0]. Line color follows region_ld_colors bins (same as markers); alpha scales by r\u00b2 \u00d7 ld_link_alpha_scale. Filter pairs with ld_link_sig_level."
      }
    },
    "ld_link_thr": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "API placeholder; minimum ld_link pair r\u00b2 is region_ld_threshold[0], not this value.",
      "default": 0.8,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Currently not read by the implementation\u2014minimum link r\u00b2 is region_ld_threshold[0]; set bins via region_ld_threshold instead."
      }
    },
    "ld_link_color": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "API placeholder; ld_link colors follow region_ld_colors, not this parameter.",
      "default": "blue",
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Currently unused\u2014line colors match region_ld_threshold/region_ld_colors bins."
      }
    },
    "ld_link_alpha_scale": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Scale line alpha as min(r\u00b2 \u00d7 scale, 1.0) for ld_link segments.",
      "default": 0.2,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Higher values make high-LD links more opaque."
      }
    },
    "ld_link_linewidth": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Line width for all ld_link segments.",
      "default": 1.0,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Fixed width; color/alpha still reflect LD bin and r\u00b2."
      }
    },
    "ld_link_sig_level": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "P-value cutoff for ld_link pairs; at least one variant in the pair must pass.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "Defaults to sig_level when None. Independent from anno_sig_level."
      }
    },
    "show_legend": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Show figure-level legend below phenogram",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "show_ld_score": {
      "plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r"
      ],
      "desc": "Annotate reference variants with LD score and draw LD-scored links.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": true,
      "ctx_desc": {
        "plot_region:r": "LD score = sum of r\u00b2 to other variants; requires vcf_path or ld_path."
      }
    },
    "legend1": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Toggle first legend block",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend2": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Toggle second legend block",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend_kwargs": {
      "plots": [
        "compare_effect",
        "plot_phenogram"
      ],
      "desc": "Legend styling kwargs",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend_ncol": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Number of columns in phenogram figure legend",
      "default": 6,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend_mode": {
      "plots": [
        "compare_effect",
        "plot_effect"
      ],
      "desc": "Legend layout: int code (plot_effect) or string mode (compare_effect).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend_pos": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Legend position",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend_title": {
      "plots": [
        "compare_effect",
        "plot_pipcs"
      ],
      "desc": "Legend title",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "legend_title2": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Second legend title",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "locus": {
      "plots": [
        "plot_pipcs"
      ],
      "desc": "Locus label for credible sets",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "log": {
      "plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_rg",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Logger object",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Minor allele frequency column",
      "default": "MAF",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf_bin_colors": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Colors for MAF bins",
      "default": [
        "#f0ad4e",
        "#5cb85c",
        "#5bc0de",
        "#000042"
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf_bins": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "MAF bin definitions for stratified QQ",
      "default": [
        [
          0,
          0.01
        ],
        [
          0.01,
          0.05
        ],
        [
          0.05,
          0.25
        ],
        [
          0.25,
          0.5
        ]
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "maf_stratify"
    },
    "maf_level": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Minor allele frequency stratification level",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf_range": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "MAF range for power computation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_size": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_snp_density:b",
        "plot_phenogram"
      ],
      "desc": "Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.",
      "ctx_desc": {
        "plot_mqq:r": "Regional plot sizes for non-lead and lead variants.",
        "plot_region:r": "Tuple (small, large) for non-lead vs lead/significant tiers on the locus scatter; reference overlay uses ~1.5\u00d7 max.",
        "plot_mqq:mqq": "Manhattan marker sizes for non-significant and significant variants."
      },
      "default": null,
      "ctx_defaults": {
        "plot_phenogram": 81,
        "plot_mqq:r": [
          40,
          65
        ],
        "plot_region": [
          40,
          65
        ],
        "plot_mqq:mqq": [
          5,
          20
        ],
        "plot_miami2": [
          5,
          20
        ]
      },
      "add_to_docstring": false
    },
    "marker_color_map": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Map from phenogram anno_color values to marker colors",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_gap_pt": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Horizontal gap between phenogram markers within a group, in points",
      "default": 3,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_shape_map": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Map from phenogram anno_shape values to matplotlib marker codes",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_label_gap_pt": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Vertical gap between phenogram marker row and text label below, in points",
      "default": 2.75,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_label_align": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Horizontal alignment of phenogram marker label relative to marker row (center, left, right)",
      "default": "center",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_fontsize": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Font size for phenogram marker-mode text labels",
      "default": 11,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_linewidth": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Edge linewidth for phenogram marker scatter points",
      "default": 0.6,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_label_bbox": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "If True, draw phenogram marker labels with a white text outline (no filled box)",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "group_min_vertical_gap_pt": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Minimum vertical spacing between phenogram group annotation blocks, in points",
      "default": 3.5,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "group_marker_to_marker_gap_pt": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Minimum spacing between marker rows of adjacent phenogram groups, in points",
      "default": 3,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "group_label_box_pad_pt": {
      "plots": [
        "plot_phenogram"
      ],
      "desc": "Extra padding around phenogram label text for overlap calculations, in points",
      "default": 1.5,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "markercolor": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Base marker color",
      "default": "#597FBD",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "math_fontfamily": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Math text font family",
      "default": "dejavusans",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mlog10p": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq",
        "plot_region:r"
      ],
      "desc": "Negative log10 p-value column; improves performance and stability if provided",
      "ctx_desc": {
        "plot_region:r": "-log10(P) values for y-axis in regional plot",
        "plot_mqq": "-log10(P) values driving Manhattan heights and QQ distribution",
        "plot_qq:qq": "Observed -log10(P) used against expected under null in QQ plot"
      },
      "default": "MLOG10P",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mode": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_stacked_mqq",
        "plot_power",
        "plot_power:q",
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Plot layout mode. Values depend on the plot function; see ctx_desc.",
      "ctx_desc": {
        "plot_mqq:mqq": "Combined Manhattan (left) and QQ (right); default for plot_mqq().",
        "plot_mqq:m": "Manhattan plot only.",
        "plot_mqq:qq": "QQ plot only.",
        "plot_mqq:r": "Regional locus plot; requires region=(chr, start, end). Prefer plot_region().",
        "plot_mqq:b": "Brisbane SNP-density layout (legacy; prefer plot_snp_density()).",
        "plot_snp_density:b": "Brisbane SNP-density layout (mode is forced to b).",
        "plot_trumpet:q": "Quantitative trait mode; power lines computed for continuous effect sizes",
        "plot_trumpet:b": "Binary trait mode; power lines computed under case-control assumptions"
      },
      "default": null,
      "ctx_defaults": {
        "plot_trumpet:q": "q",
        "plot_trumpet:b": "b",
        "plot_stacked_mqq": "r"
      },
      "add_to_docstring": false
    },
    "mqqratio": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Layout ratio for combined Manhattan-QQ plot",
      "default": 3,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "mqq_layout"
    },
    "mtitle": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Manhattan title",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mtitle_pad": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Manhattan title padding",
      "default": 1.08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mysumstats": {
      "plots": [],
      "desc": "",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "n": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Sample size column (quantitative mode)",
      "ctx_desc": {
        "plot_trumpet:q": "Total sample size used to compute power envelopes in quantitative mode"
      },
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "n_matrix": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Power curve smoothness parameter",
      "default": 1000,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ncase": {
      "plots": [
        "plot_trumpet:b"
      ],
      "desc": "Case count (binary mode)",
      "ctx_desc": {
        "plot_trumpet:b": "Number of cases in study for binary mode power envelopes"
      },
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ncol": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Number of columns in legend",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ncontrol": {
      "plots": [
        "plot_trumpet:b"
      ],
      "desc": "Control count (binary mode)",
      "ctx_desc": {
        "plot_trumpet:b": "Number of controls in study for binary mode power envelopes"
      },
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "nea": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Non-effect allele column",
      "default": "NEA",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "null_beta": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Null beta for hypothesis testing",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "onlycs": {
      "plots": [
        "plot_pipcs"
      ],
      "desc": "Plot only variants assigned to a credible set.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_pipcs": "When True, plot only CS-assigned variants."
      }
    },
    "or_to_rr": {
      "plots": [
        "plot_trumpet:b"
      ],
      "desc": "Convert OR to RR",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "p": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq",
        "plot_region:r",
        "plot_rg",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "P-value column",
      "default": "P",
      "ctx_defaults": {
        "plot_rg": "p"
      },
      "add_to_docstring": false
    },
    "p1": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Trait column 1",
      "default": "p1",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "p2": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Trait column 2",
      "default": "p2",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "p_level": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "P-value threshold for inclusion",
      "default": 5e-08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "palette": {
      "plots": [],
      "desc": "Color palette name or list",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "panno": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Enable p-value annotation",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "panno_kwargs": {
      "plots": [
        "plot_rg"
      ],
      "desc": "P-value annotation kwargs",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "panno_texts": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Texts for p-value annotation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "pinpoint": {
      "plots": [
        "plot_manhattan",
        "plot_snp_density",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:b",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:qq",
        "plot_qq",
        "plot_qq:qq",
        "plot_mqq:r",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "desc": "Variants to pinpoint",
      "default": [],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_region",
        "plot_region:r",
        "plot_mqq:r"
      ],
      "no_plots_group": "pinpoint"
    },
    "pinpoint_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Color for pinpoint",
      "default": "red",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "pip": {
      "plots": [
        "plot_pipcs"
      ],
      "desc": "Column name for posterior inclusion probability.",
      "default": "PIP",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_pipcs": "PIP column in finemapping results."
      }
    },
    "pipcs_raw": {
      "plots": [],
      "desc": "",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "pos": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Base-pair position column used with `chrom` for plotting",
      "add_to_docstring": false,
      "default": "POS",
      "ctx_defaults": {}
    },
    "prevalence": {
      "plots": [
        "plot_trumpet:b"
      ],
      "desc": "Disease prevalence (used for power lines in binary mode)",
      "ctx_desc": {
        "plot_trumpet:b": "Population disease prevalence parameter for binary mode power computation"
      },
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "q_level": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Quantile level for thresholds",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qq_line_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Reference line color for QQ plot (e.g., 'grey')",
      "default": "grey",
      "ctx_defaults": {
        "plot_qq:qq": "grey"
      },
      "add_to_docstring": false
    },
    "qq_scatter_kwargs": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_qq:qq"
      ],
      "desc": "Style dict for QQ scatter (e.g., marker, s, edgecolor)",
      "default": {},
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qq_xlabels": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Custom x-axis tick labels for QQ plot",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qq_xlim": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "X-axis limits for QQ plot, e.g., (min, max)",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qqscatterargs": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "QQ scatter kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qtitle": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Manhattan/QQ combined title",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_mqq:r",
        "plot_region",
        "plot_region:r",
        "plot_snp_density",
        "plot_snp_density:b"
      ],
      "no_plots_group": "qq_panel"
    },
    "qtitle_pad": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "QQ title padding",
      "default": 1.08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "r2": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Show R-squared value",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "r2_kwargs": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Text kwargs for R^2 annotation in AF comparison",
      "default": {
        "va": "bottom",
        "ha": "right"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "r_or_r2": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Show r or r^2 statistic",
      "default": "r2",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "r_se": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Show regression standard error",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "raf": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Column name for reference allele frequency.",
      "default": "RAF",
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_daf": "Reference allele frequency column."
      }
    },
    "ref_chrom": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Reference chromosome column",
      "default": "REF_CHR",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ref_pos": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Reference position column",
      "default": "REF_START",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "reg_box": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Draw regression stats box",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "reg_line_kwargs": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Regression line styling for AF comparison",
      "default": {
        "color": "#cccccc",
        "linestyle": "--"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "reg_text": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Custom text for regression box",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_region:r"
      ],
      "desc": "Genomic locus as (chr, start, end) in base pairs.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:b",
        "plot_mqq:qq",
        "plot_qq",
        "plot_qq:qq",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_miami2"
      ],
      "no_plots_group": "region_panel",
      "ctx_desc": {
        "plot_region:r": "Required locus for plot_region(). Example: (7, 156538803, 157538803). Use get_region_start_and_end() to derive windows.",
        "plot_mqq:r": "Same as plot_region(); required when mode='r'."
      }
    },
    "region_anno_bbox_kwargs": {
      "plots": [
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Annotation bbox kwargs for region",
      "default": {
        "ec": "None",
        "fc": "None"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_flank_factor": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Fraction of locus width added as padding on each side.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Expands (start, end) symmetrically before plotting."
      }
    },
    "region_grid": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Vertical grid lines at genomic tick positions on the locus scatter panel.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Styled with region_grid_line."
      }
    },
    "region_grid_line": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Grid line style for regional plot",
      "default": {
        "linewidth": 2,
        "linestyle": "--"
      },
      "ctx_defaults": {
        "plot_region:r": {
          "linewidth": 2,
          "linestyle": "--"
        }
      },
      "add_to_docstring": false
    },
    "region_hspace": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Vertical gap between scatter, recombination, and gene tracks.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Matplotlib hspace between ax1/ax3/ax4 panels."
      }
    },
    "region_ld_colors": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Colors for LD r\u00b2 bins (single-reference); paired with region_ld_threshold.",
      "default": [
        "#E4E4E4",
        "#020080",
        "#86CEF9",
        "#24FF02",
        "#FDA400",
        "#FF0000",
        "#FF0000"
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "List length = len(region_ld_threshold)+3. Index 0: no/missing LD; indices 1\u2026N: LD intervals between thresholds; last index: reference/lead variant. Default 7 colors for 4 thresholds. ld_link reuses these colors."
      }
    },
    "region_ld_colors_m": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Base colors for multi-reference LD coloring (one entry per region_ref).",
      "default": [
        "#E51819",
        "#367EB7",
        "green",
        "#F07818",
        "#AD5691",
        "yellow",
        "purple"
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "When len(region_ref)>1, each color builds a white\u2192color gradient across the same bins as region_ld_threshold. Variant shape comes from region_marker_shapes[1+] per reference, not from LD tier."
      }
    },
    "region_ld_legend": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "no_plots": [
        "plot_stacked_mqq"
      ],
      "desc": "Show LD r\u00b2 colorbar inset beside the locus panel.",
      "default": true,
      "ctx_defaults": {
        "plot_region:r": true
      },
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "True when vcf_path or ld_path supplies LD; uses region_ld_threshold/colors legend."
      }
    },
    "region_ld_threshold": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "LD r\u00b2 cutoffs (single-reference) that define color bins for scatter markers and ld_link lines.",
      "default": [
        0.2,
        0.4,
        0.6,
        0.8
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Ascending r\u00b2 boundaries, e.g. [0.2, 0.4, 0.6, 0.8]. Bins: missing/0, (0\u2192t0], (t0\u2192t1], \u2026, (t_last\u21921], plus reference/lead. Pair with region_ld_colors (len = len(thresholds)+3). ld_link draws pairs with r\u00b2 \u2265 thresholds[0]."
      }
    },
    "region_lead_grid": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "no_plots": [
        "plot_stacked_mqq"
      ],
      "desc": "Highlight line at the reference/lead variant genomic position.",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Styled with region_lead_grid_line (default red dashed)."
      }
    },
    "region_lead_grid_line": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Matplotlib kwargs for the reference/lead vertical guide line.",
      "default": {
        "alpha": 0.5,
        "linewidth": 2,
        "linestyle": "--",
        "color": "#FF0000"
      },
      "ctx_defaults": {
        "plot_region:r": {
          "alpha": 0.5,
          "linewidth": 2,
          "linestyle": "--",
          "color": "#FF0000"
        }
      },
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Default: red dashed, alpha 0.5, linewidth 2. Used when region_lead_grid=True."
      }
    },
    "region_legend_marker": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Draw the reference-variant marker symbol in the LD colorbar inset.",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Uses region_marker_shapes[2] (single-ref) inside the colorbar when True."
      }
    },
    "region_marker_shapes": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Matplotlib marker shapes by role; LD r\u00b2 sets color only (region_ld_threshold/colors), not shape.",
      "default": [
        "X",
        "o",
        "^",
        "s",
        "D",
        "*",
        "P",
        "h",
        "8"
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Shape by index; LD r\u00b2 controls color via region_ld_threshold/region_ld_colors, not shape. Index 0: missing LD (default 'X'). Index 1: variants with LD data. Index 2+: reference variant(s)\u2014single-ref uses index 2; multi-ref uses 2, 3, \u2026 Do not set scatter_kwargs['marker']."
      }
    },
    "region_protein_coding": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Show only protein-coding genes on the GTF annotation track.",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Applies when gtf_path is set (or 'default')."
      }
    },
    "region_recombination": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Plot recombination-rate track under the locus (requires rr_path).",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Uses rr_path, rr_lim, rr_ylabel; disable to hide the RR panel."
      }
    },
    "region_ref": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Reference variant ID(s) for LD coloring relative to vcf_path/ld_path.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "SNPID or rsID list, e.g. ['rs123']. None or [None] auto-picks the lead variant. Up to 7 refs; multi-ref switches to region_ld_colors_m."
      }
    },
    "region_ref_alias": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Map reference variant IDs to display labels in legend/colorbar.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Dict {variant_id: label} for colorbar/legend text."
      }
    },
    "region_ref_second": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Legacy second reference ID; prefer multiple entries in region_ref.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Deprecated pattern\u2014include all references in region_ref instead."
      }
    },
    "region_step": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_panels",
        "plot_region:r",
        "plot_stacked_mqq"
      ],
      "desc": "Number of major tick intervals on the locus x-axis.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Default 21 tick steps across the plotted window."
      },
      "no_plots_group": "panel_layout"
    },
    "region_title": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Custom title above the locus scatter panel.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "None auto-builds from region and lead variant; pass through region_title_args/kwargs."
      }
    },
    "region_title_kwargs": {
      "plots": [
        "plot_stacked_mqq",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Regional plot title styling args",
      "default": {
        "family": "Arial",
        "size": 12
      },
      "ctx_defaults": {
        "plot_region:r": {
          "family": "Arial"
        }
      },
      "add_to_docstring": false
    },
    "rename_dic": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Rename dictionary for labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "repel_force": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_region:r"
      ],
      "desc": "Text repulsion force parameter",
      "default": 0.03,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rg": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Genetic correlation value column",
      "default": "rg",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rganno": {
      "plots": [
        "plot_rg"
      ],
      "desc": "RG annotation mode",
      "default": "non",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rganno_kwargs": {
      "plots": [
        "plot_rg"
      ],
      "desc": "RG annotation kwargs",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_chr_dict": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Recombination rate chrom dict",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_header_dict": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Recombination rate header dict",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_lim": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Y-axis limits (cM/Mb) for the recombination track.",
      "default": [
        0,
        100
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Tuple (min, max); default (0, 100)."
      }
    },
    "rr_path": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Recombination-rate resource path or 'default'.",
      "default": "default",
      "ctx_defaults": {
        "plot_region:r": "default"
      },
      "add_to_docstring": false,
      "no_plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:b",
        "plot_mqq:qq",
        "plot_qq",
        "plot_qq:qq",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q",
        "plot_miami2"
      ],
      "no_plots_group": "rr",
      "ctx_desc": {
        "plot_region:r": "Used when region_recombination=True; y-axis limits from rr_lim."
      }
    },
    "rr_ylabel": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Whether to show the recombination-rate y-axis label.",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Applies to the RR panel when region_recombination=True."
      }
    },
    "same_ylim": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "Use same ylim across panels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "save": {
      "plots": [
        "compare_effect",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq",
        "plot_pipcs",
        "plot_region:r",
        "plot_rg",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Boolean or output filepath; when boolean, uses default naming",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "save_kwargs": {
      "plots": [
        "compare_effect",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq",
        "plot_pipcs",
        "plot_region:r",
        "plot_rg",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Save kwargs for GW heatmap",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "saveargs": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Save kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sc_linewidth": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Line width for significance lines",
      "default": 2,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scaled": {
      "plots": [
        "compare_effect",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Auto-detected when scaled effect columns exist; not a direct plot kwarg.",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scaled1": {
      "plots": [
        "compare_effect",
        "plot_miami2"
      ],
      "desc": "Study-1 scaling flag (legacy registry entry; detected from columns).",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scaled2": {
      "plots": [
        "compare_effect",
        "plot_miami2"
      ],
      "desc": "Study-2 scaling flag (legacy registry entry; detected from columns).",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scatter_kwargs": {
      "plots": [
        "compare_effect",
        "plot_daf",
        "plot_effect",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_pipcs",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size.",
      "ctx_desc": {
        "plot_mqq:mqq": "Manhattan/QQ scatter styling.",
        "plot_mqq:r": "Regional scatter styling; marker_size sets point sizes.",
        "plot_gwheatmap": "Scatter kwargs for GWAS heatmap points.",
        "plot_region:r": "Extra kwargs for locus scatter points. Do not set 's' (use marker_size) or 'marker' (use region_marker_shapes)."
      },
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scatter_kwargs_outlier": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Scatter kwargs for outlier points in AF comparison",
      "default": {
        "s": 3,
        "c": "red"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scatterargs": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Scatter kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "se": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Standard error column",
      "default": "SE",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sig_level": {
      "plots": [
        "compare_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Significance threshold for reference line and marker sizing",
      "default": 5e-08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_sig_level": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram"
      ],
      "desc": "Significance level for extracting lead variants to annotate. Can be set independently from sig_level.",
      "default": 5e-08,
      "ctx_defaults": {},
      "add_to_docstring": true
    },
    "sig_levels": {
      "plots": [
        "plot_rg",
        "plot_power",
        "plot_power:q",
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Significance levels",
      "default": [
        0.05
      ],
      "ctx_defaults": {
        "plot_power": 5e-08,
        "plot_power:q": 5e-08,
        "plot_power:b": 5e-08,
        "plot_power_x": 5e-08
      },
      "add_to_docstring": false
    },
    "sig_line": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Whether to draw significance reference line",
      "default": true,
      "ctx_defaults": {
        "plot_mqq": true,
        "plot_region:r": true
      },
      "add_to_docstring": false
    },
    "sig_line_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Significance line color",
      "default": "grey",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "size": {
      "plots": [
        "plot_effect",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Size mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sizes": {
      "plots": [
        "plot_gwheatmap",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Size list for style mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sizes_gw": {
      "plots": [],
      "desc": "Marker size range for GW heatmap",
      "default": [
        10,
        50
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "skip": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Minimum -log10(P) for variants shown on the plot (variants below this are omitted).",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snpid": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "SNP identifier column",
      "default": "SNPID",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snplist": {
      "plots": [
        "compare_effect"
      ],
      "desc": "List of SNPs to include",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snpr2": {
      "plots": [
        "plot_effect"
      ],
      "desc": "SNP r2 column",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snpr2_kwargs": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Styling kwargs for SNP r2 panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snpr2_label": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Label for SNP r2 panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snpvar_panel": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Toggle SNP variance panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sort": {
      "plots": [
        "plot_associations"
      ],
      "desc": "Sorting key or method",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sort_key": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Sort key function",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sort_kwargs": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Sorting kwargs",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "square": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Square cells toggle",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "stratified": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Enable stratified QQ by MAF",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "style": {
      "plots": [],
      "desc": "Deprecated; not used by plot_trumpet implementation.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "suggestive_sig_level": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Suggestive threshold value, e.g., 5e-6",
      "default": 5e-06,
      "ctx_defaults": {
        "plot_mqq": 5e-06
      },
      "add_to_docstring": false
    },
    "suggestive_sig_line": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Whether to draw suggestive threshold line (e.g., 5e-6)",
      "default": false,
      "ctx_defaults": {
        "plot_mqq": false
      },
      "add_to_docstring": false
    },
    "suggestive_sig_line_color": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Suggestive significance line color",
      "default": "grey",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sumstats": {
      "plots": [
        "plot_ld_block"
      ],
      "desc": "Sumstats or DataFrame for LD block when using vcf_path+region.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "tabix": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Tabix index path for fast IO",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "taf": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_track"
      ],
      "desc": "Track arrangement factors",
      "default": [
        4,
        0,
        0.95,
        1,
        1
      ],
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "track_panel"
    },
    "threshold": {
      "plots": [
        "plot_daf"
      ],
      "desc": "AF difference threshold",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "threshold_line_kwargs": {
      "plots": [
        "plot_daf"
      ],
      "desc": "Threshold helper line styling for AF comparison",
      "default": {
        "color": "#cccccc",
        "linestyle": "dotted"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "title": {
      "plots": [
        "plot_effect",
        "plot_sankey",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq",
        "plot_region:r",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Figure title text",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "title_fontsize": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Title font size",
      "default": 13,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "title_kwargs": {
      "plots": [
        "plot_panels"
      ],
      "desc": "Title styling kwargs (e.g., family, fontsize, weight)",
      "default": null,
      "ctx_defaults": {
        "plot_mqq": {
          "family": "Arial"
        },
        "plot_region:r": {
          "family": "Arial"
        },
        "plot_stacked": {
          "family": "Arial"
        },
        "plot_template": {
          "family": "Arial"
        }
      },
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "title_pad": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Title padding",
      "default": 1.08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "title_pos": {
      "plots": [
        "plot_panels",
        "plot_stacked_mqq"
      ],
      "desc": "Title position in axes coordinates (x, y)",
      "default": null,
      "ctx_defaults": {
        "plot_panels": "left",
        "plot_stacked_mqq": [
          0.01,
          0.97
        ]
      },
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "titles": {
      "plots": [
        "plot_miami2",
        "plot_panels"
      ],
      "desc": "Pair plot titles",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "titles_pad": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "Title padding configuration",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "to_plot": {
      "plots": [],
      "desc": "",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_exon_ratio": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Exon track ratio",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_font_family": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Font family for region tracks",
      "default": "Arial",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_fontsize_ratio": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Track fontsize ratio",
      "default": 0.95,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_n": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Maximum gene annotation rows (tracks) in the GTF panel.",
      "default": 4,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Genes beyond this limit are omitted; adjust track_n_offset for spacing."
      }
    },
    "track_n_offset": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Track offset",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_text_offset": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Track text offset",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ts": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Power thresholds to plot",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "use_rank": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_snp_density:b"
      ],
      "desc": "Use rank for chrom indexing",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "values": {
      "plots": [
        "plot_associations"
      ],
      "desc": "Value to plot in associations heatmap",
      "default": "Beta",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "vcf_chr_dict": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Chromosome mapping for VCF resource",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "vcf_path": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Reference-panel VCF for LD r\u00b2 computation.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "ctx_desc": {
        "plot_region:r": "Required for LD-colored scatter, ld_block, and ld_link unless ld_path is provided. Biallelic unphased VCF is supported."
      }
    },
    "verbose": {
      "plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_sankey",
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs",
        "plot_qq:qq",
        "plot_region:r",
        "plot_rg",
        "plot_snp_density:b",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Verbose logging toggle",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "wc_correction": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Winner's curse correction toggle",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "wc_sig_level": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Significance threshold for WC correction",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "windowsizekb": {
      "plots": [
        "plot_manhattan",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r"
      ],
      "desc": "Window size for lead variant extraction (kb)",
      "default": 500,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "x": {
      "plots": [
        "plot_effect"
      ],
      "desc": "X variable/column name",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xchrpad": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Chrom padding for x grouping",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlabel": {
      "plots": [
        "plot_associations",
        "plot_daf",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "X-axis label",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlabel_coords": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "X label position adjustment",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlim": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "X-axis limits",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlim_eaf": {
      "plots": [
        "plot_effect"
      ],
      "desc": "X limits for EAF panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlim_snpr2": {
      "plots": [
        "plot_effect"
      ],
      "desc": "X limits for SNP r2 panel",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xpad": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "X padding proportion",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xpadl": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Left X padding",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xpadr": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Right X padding",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xscale": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "X-axis scale",
      "default": "log",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtick_chr_dict": {
      "plots": [
        "plot_gwheatmap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_pipcs"
      ],
      "desc": "X-axis tick chromosome mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtick_chr_dict_gw": {
      "plots": [],
      "desc": "Tick chr dict for x axis",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtick_label_pad": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "Pad between x tick and label",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtick_label_size": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "X tick label size",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xticklabel_kwargs": {
      "plots": [
        "plot_rg"
      ],
      "desc": "X ticklabel kwargs",
      "default": {
        "rotation": 45,
        "horizontalalignment": "left",
        "verticalalignment": "bottom",
        "fontsize": 10,
        "fontfamily": "Arial"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xticklabels": {
      "plots": [],
      "desc": "Custom x-axis tick labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtickpad": {
      "plots": [
        "plot_miami2"
      ],
      "desc": "X tick pad",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xticks": {
      "plots": [],
      "desc": "Custom x-axis ticks",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtight": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r"
      ],
      "desc": "Tight X padding",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xylabel_prefix": {
      "plots": [
        "compare_effect"
      ],
      "desc": "Prefix for axis labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "y": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Y variable/column name",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "y_sort": {
      "plots": [
        "plot_effect"
      ],
      "desc": "Y sorting key",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ychrpad": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Chrom padding for y grouping",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ylabel": {
      "plots": [
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Y-axis label",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ylabels": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Custom y-axis labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ylim": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_region:r",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Y-axis limits",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yscale_factor": {
      "plots": [
        "plot_trumpet:b",
        "plot_trumpet:q"
      ],
      "desc": "Y scale factor",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ystep": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Step size for y-axis",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ytick3": {
      "plots": [
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_qq:qq"
      ],
      "desc": "Use 3 y-axis ticks",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ytick_chr_dict": {
      "plots": [
        "plot_gwheatmap"
      ],
      "desc": "Map chromosome numbers to y-axis tick labels on GW heatmap.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ytick_chr_dict_gw": {
      "plots": [],
      "desc": "Tick chr dict for y axis",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yticklabel_kwargs": {
      "plots": [
        "plot_rg"
      ],
      "desc": "Matplotlib kwargs for LDSC rg heatmap y-axis tick labels (rotation, fontsize, \u2026).",
      "default": {
        "fontsize": 10,
        "fontfamily": "Arial"
      },
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yticklabels": {
      "plots": [],
      "desc": "Custom y-axis tick labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yticks": {
      "plots": [],
      "desc": "Custom y-axis ticks",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "beta_col": {
      "plots": [],
      "desc": "Column name for effect size in forest plot.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "se_col": {
      "plots": [],
      "desc": "Column name for standard error in forest plot.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_wrap": {
      "plots": [],
      "desc": "Enable text wrapping for phenogram annotations.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_wrap_width_pt": {
      "plots": [],
      "desc": "Max annotation line width in points (phenogram).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_wrap_chars_per_line": {
      "plots": [],
      "desc": "Character wrap width for phenogram annotations.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_max_len": {
      "plots": [],
      "desc": "Truncate phenogram annotation labels to this length.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ns": {
      "plots": [
        "plot_power",
        "plot_power:q",
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Sample size(s) for theoretical power curves.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "prevalences": {
      "plots": [
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Prevalence value(s) for binary power curves.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ncases": {
      "plots": [
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Case count(s) for binary power curves.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ncontrols": {
      "plots": [
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Control count(s) for binary power curves.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mafs": {
      "plots": [
        "plot_power",
        "plot_power:q",
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "MAF grid for plot_power_x.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "betas": {
      "plots": [
        "plot_power",
        "plot_power:q",
        "plot_power:b",
        "plot_power_x"
      ],
      "desc": "Effect-size grid for plot_power_x.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "align_xaxis": {
      "plots": [
        "plot_panels"
      ],
      "desc": "Share genomic x-axis limits across stacked panels.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "variant_positions": {
      "plots": [
        "plot_panels"
      ],
      "desc": "Genomic positions for vertical guide lines in plot_panels.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "variant_line_kwargs": {
      "plots": [
        "plot_panels"
      ],
      "desc": "Style kwargs for variant guide lines.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "panel_layout"
    },
    "region_chromatin_labels": {
      "plots": [
        "plot_chromatin"
      ],
      "desc": "Labels for each chromatin state track row.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "chromatin_panel",
      "no_plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_gwheatmap",
        "plot_ld_block",
        "plot_lead_overlap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_pipcs",
        "plot_power",
        "plot_power:b",
        "plot_power:q",
        "plot_power_x",
        "plot_qq:qq",
        "plot_region",
        "plot_region:r",
        "plot_rg",
        "plot_sankey",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_stacked_mqq",
        "plot_trumpet",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ]
    },
    "xlim_i": {
      "plots": [
        "plot_chromatin"
      ],
      "desc": "X-axis offset for chromatin track alignment.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "chromatin_panel"
    },
    "file_format": {
      "plots": [
        "plot_track"
      ],
      "desc": "Track file format override (gtf, bed, bigwig, bigbed).",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "track_panel",
      "no_plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_gwheatmap",
        "plot_ld_block",
        "plot_lead_overlap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_pipcs",
        "plot_power",
        "plot_power:b",
        "plot_power:q",
        "plot_power_x",
        "plot_qq:qq",
        "plot_region",
        "plot_region:r",
        "plot_rg",
        "plot_sankey",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_stacked_mqq",
        "plot_trumpet",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ]
    },
    "arc_height": {
      "plots": [
        "plot_arc"
      ],
      "desc": "Relative height of contact arcs above the baseline.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "arc_panel",
      "no_plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_gwheatmap",
        "plot_ld_block",
        "plot_lead_overlap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_pipcs",
        "plot_power",
        "plot_power:b",
        "plot_power:q",
        "plot_power_x",
        "plot_qq:qq",
        "plot_region",
        "plot_region:r",
        "plot_rg",
        "plot_sankey",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_stacked_mqq",
        "plot_trumpet",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ]
    },
    "max_arcs": {
      "plots": [
        "plot_arc"
      ],
      "desc": "Maximum number of arcs to draw.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "arc_panel"
    },
    "score_col": {
      "plots": [
        "plot_arc"
      ],
      "desc": "BEDPE column used to filter or color arcs by score.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "arc_panel"
    },
    "ylabel_template": {
      "plots": [
        "plot_ag_contact",
        "plot_ag_overlay",
        "plot_ag_sashimi",
        "plot_ag_tracks"
      ],
      "desc": "Format string for AlphaGenome track y-axis labels.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "ag_panel",
      "no_plots": [
        "compare_effect",
        "plot_associations",
        "plot_daf",
        "plot_effect",
        "plot_forest",
        "plot_gwheatmap",
        "plot_ld_block",
        "plot_lead_overlap",
        "plot_manhattan",
        "plot_miami2",
        "plot_mqq",
        "plot_mqq:m",
        "plot_mqq:mqq",
        "plot_mqq:qqm",
        "plot_mqq:r",
        "plot_phenogram",
        "plot_pipcs",
        "plot_power",
        "plot_power:b",
        "plot_power:q",
        "plot_power_x",
        "plot_qq:qq",
        "plot_region",
        "plot_region:r",
        "plot_rg",
        "plot_sankey",
        "plot_snp_density",
        "plot_snp_density:b",
        "plot_stacked_mqq",
        "plot_trumpet",
        "plot_trumpet:b",
        "plot_trumpet:q"
      ]
    },
    "filter_threshold": {
      "plots": [
        "plot_ag_contact",
        "plot_ag_overlay",
        "plot_ag_sashimi",
        "plot_ag_tracks"
      ],
      "desc": "Minimum value for AlphaGenome sashimi junction display.",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false,
      "no_plots_group": "ag_panel"
    }
  },
  "registry": {}
}
