{
  "args": {
    "chrom": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Chromosome column used to position variants and x-axis layout",
      "default": "CHR",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "pos": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Base-pair position column used with `chrom` for plotting",
      "add_to_docstring": false,
      "default": "POS",
      "ctx_defaults": {}
    },
    "p": {
      "plots": [["plot_rg", null], ["plot_gwheatmap", null]],
      "desc": "P-value column for RG/GW heatmap",
      "default": "p",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mlog10p": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"]],
      "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
    },
    "scaled": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Boolean indicating `mlog10p` is already precomputed",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qq_scatter_args": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Style dict for QQ scatter (e.g., marker, s, edgecolor)",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qq_line_color": {
      "plots": [["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_xlabels": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Custom x-axis tick labels for QQ plot",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qq_xlim": {
      "plots": [["plot_qq", "qq"]],
      "desc": "X-axis limits for QQ plot, e.g., (min, max)",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region": {
      "plots": [["plot_region", "r"]],
      "desc": "Region triple (chr, start, end) in base pairs",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_title": {
      "plots": [["plot_region", "r"]],
      "desc": "Title text for regional plot",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_ld_threshold": {
      "plots": [["plot_region", "r"]],
      "desc": "LD r^2 thresholds list for color stratification",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_ld_legend": {
      "plots": [["plot_region", "r"]],
      "desc": "Whether to show LD legend/colorbar",
      "default": true,
      "ctx_defaults": {
        "plot_region:r": true
      },
      "add_to_docstring": false
    },
    "region_ld_colors": {
      "plots": [["plot_region", "r"]],
      "desc": "LD colors (list or palette) aligned with thresholds",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "vcf_path": {
      "plots": [["plot_region", "r"]],
      "desc": "Reference VCF path for LD computation/loading",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_path": {
      "plots": [["plot_region", "r"]],
      "desc": "Recombination rate data path or 'default' for built-in resource",
      "default": "default",
      "ctx_defaults": {
        "plot_region:r": "default"
      },
      "add_to_docstring": false
    },
    "gtf_path": {
      "plots": [["plot_region", "r"]],
      "desc": "GTF gene annotation path or 'default' for built-in resource",
      "default": "default",
      "ctx_defaults": {
        "plot_region:r": "default"
      },
      "add_to_docstring": false
    },
    "density_color": {
      "plots": [["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
    },
    "bwindowsizekb": {
      "plots": [["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
    },
    "mode": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Trumpet plot mode: 'q' (quantitative) or 'b' (binary)",
      "ctx_desc": {
        "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"
      },
      "add_to_docstring": false
    },
    "n": {
      "plots": [["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
    },
    "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
    },
    "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
    },
    "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
    },
    "sig_line": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Whether to draw significance reference line",
      "default": true,
      "ctx_defaults": {
        "plot_mqq": true,
        "plot_region:r": true
      },
      "add_to_docstring": false
    },
    "sig_level_plot": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Significance threshold for reference line, default 5e-8",
      "default": 5e-08,
      "ctx_defaults": {
        "plot_mqq": 5e-08,
        "plot_region:r": 5e-08
      },
      "add_to_docstring": false
    },
    "suggestive_sig_line": {
      "plots": [["plot_mqq", null]],
      "desc": "Whether to draw suggestive threshold line (e.g., 5e-6)",
      "default": false,
      "ctx_defaults": {
        "plot_mqq": false
      },
      "add_to_docstring": false
    },
    "suggestive_sig_level": {
      "plots": [["plot_mqq", null]],
      "desc": "Suggestive threshold value, e.g., 5e-6",
      "default": 5e-06,
      "ctx_defaults": {
        "plot_mqq": 5e-06
      },
      "add_to_docstring": false
    },
    "title": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null]],
      "desc": "Figure title text",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fontsize": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null]],
      "desc": "Font size for ticks, labels, etc.",
      "default": 12,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "font_family": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null]],
      "desc": "Font family, e.g., 'Arial', for consistent styling",
      "default": "Arial",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "save": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null]],
      "desc": "Boolean or output filepath; when boolean, uses default naming",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "save_args": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null]],
      "desc": "Dict of save options (e.g., dpi, bbox_inches)",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "build": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Genome build (e.g., '19'/'38') for annotation/coordinate resources",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fig_args": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null]],
      "desc": "Figure kwargs (e.g., figsize, dpi)",
      "default": null,
      "ctx_defaults": {}, 
      "banned_keys": [],
      "ctx_banned_keys": [],
      "add_to_docstring": false
    },
    "figax": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"]],
      "desc": "Existing figure/axes tuple to draw on",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "colors": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"]],
      "desc": "Color palette or list",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "marker_size": {
      "plots": [["plot_mqq", null], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Marker size or size range",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ylabel": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_effect", null]],
      "desc": "Y-axis label",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlabel": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "X-axis label",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "title_pad": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"]],
      "desc": "Title padding",
      "default": 1.08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "title_fontsize": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Title font size",
      "default": 13,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "chrpad": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Chromosome padding proportion",
      "default": 0.03,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ylim": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Y-axis limits",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "dpi": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Figure DPI",
      "default": 200,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "expected_min_mlog10p": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Expected minimum -log10(P) adjustment",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "log": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null], ["plot_pipcs", null]],
      "desc": "Logger object",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "verbose": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_qq", "qq"], ["plot_snp_density", "b"], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null], ["plot_pipcs", null]],
      "desc": "Verbose logging toggle",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_title_args": {
      "plots": [["plot_region", "r"]],
      "desc": "Regional plot title styling args",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_ref": {
      "plots": [["plot_region", "r"]],
      "desc": "Reference variant(s) for LD coloring",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_ref_second": {
      "plots": [["plot_region", "r"]],
      "desc": "Second reference variant",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_grid_line": {
      "plots": [["plot_region", "r"]],
      "desc": "Grid line style for regional plot",
      "default": {
        "linewidth": 2,
        "linestyle": "--"
      },
      "ctx_defaults": {
        "plot_region:r": {
          "linewidth": 2,
          "linestyle": "--"
        }
      },
      "add_to_docstring": false
    },
    "region_lead_grid_line": {
      "plots": [["plot_region", "r"]],
      "desc": "Lead grid line style",
      "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
    },
    "region_ld_colors_m": {
      "plots": [["plot_region", "r"]],
      "desc": "LD colors for multi-lead mode",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_path": {
      "plots": [["plot_region", "r"]],
      "desc": "Path to LD matrix resource",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_map_path": {
      "plots": [["plot_region", "r"]],
      "desc": "Path to LD map file",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_fmt": {
      "plots": [["plot_region", "r"]],
      "desc": "LD format identifier (e.g., 'npz')",
      "default": "npz",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_if_square": {
      "plots": [["plot_region", "r"]],
      "desc": "Treat LD matrix as square",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_if_add_T": {
      "plots": [["plot_region", "r"]],
      "desc": "Add transpose when composing LD",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_map_rename_dic": {
      "plots": [["plot_region", "r"]],
      "desc": "Rename dictionary for LD map columns",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ld_map_kwargs": {
      "plots": [["plot_region", "r"]],
      "desc": "Extra kwargs for LD map loader",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_title": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar title",
      "default": "LD $\\mathregular{r^2}$ with variant",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_fontsize": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar font size",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_scale": {
      "plots": [["plot_region", "r"]],
      "desc": "Scale colorbar",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_font_family": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar font family",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_bbox_to_anchor": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar bbox_to_anchor",
      "default": [
        0,
        0,
        1,
        1
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_equal_aspect": {
      "plots": [["plot_region", "r"]],
      "desc": "Equal aspect for colorbar",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_w_scale": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar width scale",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_h_scale": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar height scale",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_downward_offset": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar downward offset",
      "default": 1.3,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cbar_borderpad": {
      "plots": [["plot_region", "r"]],
      "desc": "Colorbar border padding",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_n": {
      "plots": [["plot_region", "r"]],
      "desc": "Number of annotation tracks",
      "default": 4,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_n_offset": {
      "plots": [["plot_region", "r"]],
      "desc": "Track offset",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_fontsize_ratio": {
      "plots": [["plot_region", "r"]],
      "desc": "Track fontsize ratio",
      "default": 0.95,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_exon_ratio": {
      "plots": [["plot_region", "r"]],
      "desc": "Exon track ratio",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "track_text_offset": {
      "plots": [["plot_region", "r"]],
      "desc": "Track text offset",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gtf_chr_dict": {
      "plots": [["plot_region", "r"]],
      "desc": "GTF chromosome dictionary",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gtf_gene_name": {
      "plots": [["plot_region", "r"]],
      "desc": "GTF gene name column",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_header_dict": {
      "plots": [["plot_region", "r"]],
      "desc": "Recombination rate header dict",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_chr_dict": {
      "plots": [["plot_region", "r"]],
      "desc": "Recombination rate chrom dict",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_lim": {
      "plots": [["plot_region", "r"]],
      "desc": "Recombination rate limits",
      "default": [
        0,
        100
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "rr_ylabel": {
      "plots": [["plot_region", "r"]],
      "desc": "Show recombination rate y-label",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_marker_shapes": {
      "plots": [["plot_region", "r"]],
      "desc": "Marker shapes for multi-lead",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_ref_alias": {
      "plots": [["plot_region", "r"]],
      "desc": "Alias for reference variants",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_recombination": {
      "plots": [["plot_region", "r"]],
      "desc": "Plot recombination rate",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_protein_coding": {
      "plots": [["plot_region", "r"]],
      "desc": "Restrict to protein coding genes",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "region_legend_marker": {
      "plots": [["plot_region", "r"]],
      "desc": "Show legend markers",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "repel_force": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_region", "r"]],
      "desc": "Text repulsion force parameter",
      "default": 0.03,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xpad": {
      "plots": [["plot_region", "r"]],
      "desc": "X padding proportion",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xpadl": {
      "plots": [["plot_region", "r"]],
      "desc": "Left X padding",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xpadr": {
      "plots": [["plot_region", "r"]],
      "desc": "Right X padding",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtight": {
      "plots": [["plot_region", "r"]],
      "desc": "Tight X padding",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "drop_chr_start": {
      "plots": [["plot_region", "r"]],
      "desc": "Drop chromosome start",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qtitle": {
      "plots": [["plot_mqq", null]],
      "desc": "Manhattan/QQ combined title",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qtitle_pad": {
      "plots": [["plot_qq", "qq"]],
      "desc": "QQ title padding",
      "default": 1.08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "gc": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Compute genomic control lambda",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cut": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Shrink variants above threshold",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cutfactor": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Factor for shrink line",
      "default": 10,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cut_log": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Use log scale for cut line",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "skip": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Minimum -log10(P) to plot",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ystep": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Step size for y-axis",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ylabels": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Custom y-axis labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ytick3": {
      "plots": [["plot_qq", "qq"]],
      "desc": "Use 3 y-axis ticks",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "density_range": {
      "plots": [["plot_snp_density", "b"]],
      "desc": "Density value range",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "density_trange": {
      "plots": [["plot_snp_density", "b"]],
      "desc": "Threshold range",
      "default": [
        0,
        10
      ],
      "ctx_defaults": {
        "plot_snp_density:b": [
          0,
          10
        ]
      },
      "add_to_docstring": false
    },
    "density_threshold": {
      "plots": [["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_snp_density", "b"]],
      "desc": "Palette for threshold coloring",
      "default": "Blues",
      "ctx_defaults": {
        "plot_snp_density:b": "Blues"
      },
      "add_to_docstring": false
    },
    "density_palette": {
      "plots": [["plot_snp_density", "b"]],
      "desc": "Density palette",
      "default": "Reds",
      "ctx_defaults": {
        "plot_snp_density:b": "Reds"
      },
      "add_to_docstring": false
    },
    "use_rank": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_snp_density", "b"]],
      "desc": "Use rank for chrom indexing",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ts": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Power thresholds to plot",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "p_level": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "P-value threshold for inclusion",
      "default": 5e-08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_y": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Annotation y threshold",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_x": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Annotation x threshold",
      "default": 0.01,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "size": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Size mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "hue": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Hue mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "style": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Style mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scatter_args": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_daf", null], ["plot_effect", null]],
      "desc": "Scatter style kwargs",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mtitle": {
      "plots": [["plot_mqq", null]],
      "desc": "Manhattan title",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mtitle_pad": {
      "plots": [["plot_mqq", null]],
      "desc": "Manhattan title padding",
      "default": 1.08,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "snpid": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_gwheatmap", null]],
      "desc": "SNP identifier column",
      "default": "SNPID",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "eaf": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_effect", null], ["plot_gwheatmap", null]],
      "desc": "Effect allele frequency column",
      "default": "EAF",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ea": {
      "plots": [["plot_mqq", null], ["plot_gwheatmap", null]],
      "desc": "Effect allele column",
      "default": "EA",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "nea": {
      "plots": [["plot_mqq", null], ["plot_gwheatmap", null]],
      "desc": "Non-effect allele column",
      "default": "NEA",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "check": {
      "plots": [["plot_mqq", null], ["plot_gwheatmap", null]],
      "desc": "Enable input QC and normalization",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "chr_dict": {
      "plots": [["plot_mqq", null], ["plot_gwheatmap", null]],
      "desc": "Chromosome number/name mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtick_chr_dict": {
      "plots": [["plot_mqq", null], ["plot_gwheatmap", null]],
      "desc": "X-axis tick chromosome mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "vcf_chr_dict": {
      "plots": [["plot_region", "r"]],
      "desc": "Chromosome mapping for VCF resource",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "mqqratio": {
      "plots": [["plot_mqq", null]],
      "desc": "Layout ratio for combined Manhattan-QQ plot",
      "default": 3,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "windowsizekb": {
      "plots": [["plot_mqq", null]],
      "desc": "Window size for lead variant extraction (kb)",
      "default": 500,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cut_line_color": {
      "plots": [["plot_mqq", null]],
      "desc": "Color for shrink line",
      "default": "#ebebeb",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "jagged": {
      "plots": [["plot_mqq", null]],
      "desc": "Enable jagged axis break markers",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "jagged_len": {
      "plots": [["plot_mqq", null]],
      "desc": "Jagged marker length",
      "default": 0.01,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "jagged_wid": {
      "plots": [["plot_mqq", null]],
      "desc": "Jagged marker width",
      "default": 0.01,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sig_line_color": {
      "plots": [["plot_mqq", null]],
      "desc": "Significance line color",
      "default": "grey",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "additional_line": {
      "plots": [["plot_mqq", null]],
      "desc": "Additional reference lines",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "additional_line_color": {
      "plots": [["plot_mqq", null]],
      "desc": "Colors for additional lines",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sc_linewidth": {
      "plots": [["plot_mqq", null]],
      "desc": "Line width for significance lines",
      "default": 2,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "List of focal variants to highlight",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_chrpos": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Highlight by chromosome position flag",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_color": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Highlight color",
      "default": "#CB132D",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_windowkb": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Highlight window size (kb)",
      "default": 500,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_anno_args": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Annotation style kwargs for highlighted variants",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_lim": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Custom highlight limits",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "highlight_lim_mode": {
      "plots": [["plot_mqq", null], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Highlight limit mode ('absolute'|'relative')",
      "default": "absolute",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "pinpoint": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Variants to pinpoint",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "pinpoint_color": {
      "plots": [["plot_mqq", null], ["plot_region", "r"], ["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Color for pinpoint",
      "default": "red",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "stratified": {
      "plots": [["plot_mqq", null]],
      "desc": "Enable stratified QQ by MAF",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf_bins": {
      "plots": [["plot_mqq", null]],
      "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
    },
    "maf_bin_colors": {
      "plots": [["plot_mqq", null]],
      "desc": "Colors for MAF bins",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "include_chrXYMT": {
      "plots": [["plot_mqq", null]],
      "desc": "Include sex/MT chromosomes in QQ",
      "default": true,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fontfamily": {
      "plots": [["plot_mqq", null]],
      "desc": "Font family alias",
      "default": "Arial",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "math_fontfamily": {
      "plots": [["plot_mqq", null]],
      "desc": "Math text font family",
      "default": "dejavusans",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "anno_fontsize": {
      "plots": [["plot_mqq", null], ["plot_region", "r"]],
      "desc": "Font size for annotation text",
      "default": 9,
      "ctx_defaults": {
        "plot_region:r": 9,
        "plot_mqq": 9
      },
      "add_to_docstring": false
    },
    "figargs": {
      "plots": [["plot_mqq", null]],
      "desc": "Figure kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "saveargs": {
      "plots": [["plot_mqq", null]],
      "desc": "Save kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scatterargs": {
      "plots": [["plot_mqq", null]],
      "desc": "Scatter kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "qqscatterargs": {
      "plots": [["plot_mqq", null]],
      "desc": "QQ scatter kwargs alias",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "taf": {
      "plots": [["plot_region", "r"]],
      "desc": "Track arrangement factors",
      "default": [
        4,
        0,
        0.95,
        1,
        1
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "tabix": {
      "plots": [["plot_mqq", null]],
      "desc": "Tabix index path for fast IO",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Minor allele frequency column",
      "default": "MAF",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "beta": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Effect size column",
      "default": "BETA",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "maf_range": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "MAF range for power computation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "beta_range": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Beta range for power computation",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "n_matrix": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Power curve smoothness parameter",
      "default": 1000,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xscale": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "X-axis scale",
      "default": "log",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yscale_factor": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Y scale factor",
      "default": 1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "cmap": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_rg", null]],
      "desc": "Colormap selection",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xlim": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "X-axis limits",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "markercolor": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Base marker color",
      "default": "#597FBD",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sizes": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Size list for style mapping",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xticks": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Custom x-axis ticks",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xticklabels": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Custom x-axis tick labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yticks": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Custom y-axis ticks",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "yticklabels": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"]],
      "desc": "Custom y-axis tick labels",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sort": {
      "plots": [["plot_trumpet", "q"], ["plot_trumpet", "b"], ["plot_effect", null], ["plot_associations", null]],
      "desc": "Sorting key or method",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ref_chrom": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Reference chromosome column",
      "default": "REF_CHR",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ref_pos": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Reference position column",
      "default": "REF_START",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "sizes_gw": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Marker size range for GW heatmap",
      "default": [
        10,
        50
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "alpha": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Alpha for markers",
      "default": 0.5,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "group": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Grouping column for axes",
      "default": "CIS/TRANS",
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xchrpad": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Chrom padding for x grouping",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ychrpad": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Chrom padding for y grouping",
      "default": 0,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "xtick_chr_dict_gw": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Tick chr dict for x axis",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "ytick_chr_dict_gw": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Tick chr dict for y axis",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "add_b": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Add Manhattan panel below",
      "default": false,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "fig_kwargs": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Figure kwargs for GW heatmap",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "scatter_kwargs": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Scatter kwargs for GW heatmap",
      "default": null,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "height_ratios": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Panel height ratios",
      "default": [
        1,
        2
      ],
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "hspace": {
      "plots": [["plot_gwheatmap", null]],
      "desc": "Vertical space between panels",
      "default": 0.1,
      "ctx_defaults": {},
      "add_to_docstring": false
    },
    "save_kwargs": {
      "plots": [["plot_gwheatmap", null]],
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