Sumstats — Plot

Visualization methods on a loaded mysumstats object. Parameter lists match the visualization registry (help(mysumstats.plot_region)).

For top-level gl.plot_* functions, see Plotting.

plot_daf

plot_daf(**kwargs: Any) -> typing.Tuple[typing.Any, typing.Any]

Parameters:

Name	Type	Description	Default
`daf`	`str`	Discovery allele frequency column.	`'DAF'`
`eaf`	`str`	Effect allele frequency column for DAF comparison plot.	`'EAF'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [8, 4], 'dpi': 300}`
`font_kwargs`	`dict`	Font configuration kwargs.	`{'fontsize': 9}`
`helper_line_kwargs`	`dict`	45-degree helper line styling for AF comparison.	`{'color': 'black', 'linestyle': '-', 'lw': 1}`
`histplot_kwargs`	`dict`	Histogram plotting kwargs for AF distribution.	`{'log_scale': [False, False]}`
`is_45_helper_line`	`bool`	Draw 45-degree helper line.	`True`
`is_reg`	`Any`	Enable regression line computation.	required
`is_threshold`	`Any`	Draw threshold line.	required
`legend1`	`Any`	Toggle first legend block.	required
`legend2`	`Any`	Toggle second legend block.	required
`r2`	`bool`	Show R-squared value.	`False`
`r2_kwargs`	`dict`	Text kwargs for R^2 annotation in AF comparison.	`{'va': 'bottom', 'ha': 'right'}`
`raf`	`str`	Reference allele frequency column.	`'RAF'`
`reg_line_kwargs`	`dict`	Regression line styling for AF comparison.	`{'color': '#cccccc', 'linestyle': '--'}`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size.	`{'s': 1}`
`scatter_kwargs_outlier`	`dict`	Scatter kwargs for outlier points in AF comparison.	`{'s': 3, 'c': 'red'}`
`threshold`	`Any`	AF difference threshold.	required
`threshold_line_kwargs`	`dict`	Threshold helper line styling for AF comparison.	`{'color': '#cccccc', 'linestyle': 'dotted'}`
`verbose`	`bool`	Verbose logging toggle.	`True`
`xlabel`	`Any`	X-axis label.	required
`ylabel`	`Any`	Y-axis label.	required

plot_gwheatmap

plot_gwheatmap(**kwargs: Any) -> typing.Any

Genome-wide association heatmap across traits or loci. Additional Manhattan-style kwargs are forwarded via mqq_kwargs inside the implementation.

Parameters:

Name	Type	Description	Default
`add_b`	`bool`	Add Manhattan panel below.	`False`
`alpha`	`float`	Alpha for markers.	`0.5`
`check`	`bool`	Enable input QC and normalization.	`True`
`chr_dict`	`Any`	Chromosome number/name mapping.	required
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`cis_windowsizekb`	`int`	Cis-window half-width (kb) for rows in the GWAS heatmap.	`100`
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`ea`	`str`	Effect allele column.	`'EA'`
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`grid_linecolor`	`str`	Grid line color.	`'grey'`
`grid_linewidth`	`int`	Grid linewidth.	`1`
`group`	`str`	Grouping column for axes.	`'CIS/TRANS'`
`mlog10p`	`str`	Negative log10 p-value column; improves performance and stability if provided.	`'MLOG10P'`
`nea`	`str`	Non-effect allele column.	`'NEA'`
`p`	`str`	P-value column.	`'P'`
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`ref_chrom`	`str`	Reference chromosome column.	`'REF_CHR'`
`ref_pos`	`str`	Reference position column.	`'REF_START'`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	`True`
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`scaled`	`bool`	Auto-detected when scaled effect columns exist; not a direct plot kwarg.	`False`
`scatter_kwargs`	`dict`	Scatter kwargs for GWAS heatmap points.	required
`sizes`	`Any`	Size list for style mapping.	required
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`use_rank`	`bool`	Use rank for chrom indexing.	`False`
`verbose`	`bool`	Verbose logging toggle.	`True`
`xchrpad`	`int`	Chrom padding for x grouping.	`0`
`xtick_chr_dict`	`Any`	X-axis tick chromosome mapping.	required
`ychrpad`	`int`	Chrom padding for y grouping.	`0`
`ytick_chr_dict`	`Any`	Map chromosome numbers to y-axis tick labels on GW heatmap.	required

plot_mqq

plot_mqq(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Combined Manhattan–QQ plot by default; set mode for other layouts. For mode-specific parameter lists use plot_manhattan(), plot_qq(), plot_region(), or plot_snp_density().

Parameters:

Name	Type	Description	Default
`mode`	`str`	Plot layout mode. Values depend on the plot function; see ctx_desc.	`'mqq'`
`build`	`str`	Genome build (e.g., '19'/'38') for annotation/coordinate resources.	`None`
`sig_level`	`float`	Significance threshold for reference line and marker sizing.	`5e-08`
`anno_sig_level`	`float`	Significance level for extracting lead variants to annotate. Can be set independently from sig_level.	`5e-08`
`skip`	`int`	Minimum -log10(P) for variants shown on the plot (variants below this are omitted).	`0`
`cut`	`int`	Cap variant -log10(P) display above this value (squashes extreme peaks for layout).	`0`
`marker_size`	`list`	Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.	`[5, 20]`
`additional_line`	`Any`	Additional reference lines.	required
`additional_line_color`	`str or list`	Colors for additional lines.	required
`anno`	`DataFrame or list`	Annotation source or column (e.g., 'GENENAME', True, or column name).	required
`anno_adjust`	`bool`	Enable annotation position adjustment.	`False`
`anno_alias`	`dict`	Mapping from SNPID to custom annotation label.	`{}`
`anno_d`	`dict`	Per-annotation positioning options (e.g., left/right).	`{}`
`anno_fixed_arm_length`	`Any`	Fixed arm length for annotations.	required
`anno_fontsize`	`int`	Font size for annotation text.	`9`
`anno_gtf_path`	`str`	Custom GTF path for annotations.	required
`anno_height`	`int`	Height for annotations.	`1`
`anno_kwargs`	`dict`	Default styling kwargs for annotations.	`{}`
`anno_kwargs_single`	`dict`	Per-SNP styling kwargs for annotations.	`{}`
`anno_max_iter`	`int`	Maximum iterations for text repulsion algorithm.	`100`
`anno_max_rows`	`int`	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.	`40`
`anno_set`	`list`	Set of variant IDs to annotate.	`[]`
`anno_source`	`str`	Annotation source backend (e.g., 'ensembl', 'refseq').	`'ensembl'`
`anno_style`	`str`	Annotation style ('right', 'tight', 'expand').	`'right'`
`anno_xshift`	`Any`	X-axis shift applied to annotations.	required
`arm_offset`	`Any`	Offset for annotation arms.	required
`arm_scale`	`int`	Scaling factor for arm length.	`1`
`arm_scale_d`	`dict`	Per-annotation arm scaling dict.	`{}`
`arrow_kwargs`	`dict`	Arrow styling kwargs for annotations.	`{}`
`bwindowsizekb`	`int`	Window size in kilobases for density computation.	`100`
`check`	`bool`	Enable input QC and normalization.	`True`
`chr_dict`	`Any`	Chromosome number/name mapping.	required
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`chrpad`	`float`	Chromosome padding proportion.	`0.03`
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`cut_line_color`	`str or list`	Color for shrink line.	required
`cut_log`	`bool`	Use log scale for cut line.	`False`
`cutfactor`	`int`	Factor for shrink line.	`10`
`density_color`	`str or list`	Density palette or boolean to control density track colors.	required
`density_palette`	`str`	Density palette.	`'Reds'`
`density_range`	`Any`	Density value range.	required
`density_threshold`	`int`	Threshold for density highlighting.	`5`
`density_tpalette`	`str`	Palette for threshold coloring.	`'Blues'`
`density_trange`	`list`	Threshold range.	`[0, 10]`
`dpi`	`int`	Figure DPI.	`200`
`drop_chr_start`	`bool`	Drop chromosome start.	`False`
`ea`	`str`	Effect allele column.	`'EA'`
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`expected_min_mlog10p`	`int`	Expected minimum -log10(P) adjustment.	`0`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [15, 5], 'dpi': 200}`
`figax`	`Any`	Existing figure/axes tuple to draw on.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontfamily`	`str`	Font family alias.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`10`
`gc`	`bool`	Compute genomic control lambda.	`True`
`highlight`	`list`	List of focal variants to highlight.	`[]`
`highlight_anno_kwargs`	`dict`	Annotation style kwargs for highlighted variants.	`{}`
`highlight_chrpos`	`bool`	Highlight by chromosome position flag.	`False`
`highlight_color`	`str or list`	Highlight color.	required
`highlight_lim`	`Any`	Custom highlight limits.	required
`highlight_lim_mode`	`str`	Highlight limit mode ('absolute'\|'relative').	`'absolute'`
`highlight_windowkb`	`int`	Highlight window size (kb).	`500`
`include_chrXYMT`	`bool`	Include sex/MT chromosomes in QQ.	`True`
`jagged`	`bool`	Enable jagged axis break markers.	`False`
`jagged_len`	`float`	Jagged marker length.	`0.01`
`jagged_wid`	`float`	Jagged marker width.	`0.01`
`maf_bin_colors`	`str or list`	Colors for MAF bins.	required
`maf_bins`	`list`	MAF bin definitions for stratified QQ.	`[[0, 0.01], [0.01, 0.05], [0.05, 0.25], [0.25, 0.5]]`
`math_fontfamily`	`str`	Math text font family.	`'dejavusans'`
`mlog10p`	`str`	-log10(P) values driving Manhattan heights and QQ distribution.	`'MLOG10P'`
`mqqratio`	`int`	Layout ratio for combined Manhattan-QQ plot.	`3`
`mtitle`	`Any`	Manhattan title.	required
`mtitle_pad`	`float`	Manhattan title padding.	`1.08`
`nea`	`str`	Non-effect allele column.	`'NEA'`
`p`	`str`	P-value column.	`'P'`
`pinpoint`	`list`	Variants to pinpoint.	`[]`
`pinpoint_color`	`str or list`	Color for pinpoint.	required
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`qq_line_color`	`str or list`	Reference line color for QQ plot (e.g., 'grey').	required
`qq_scatter_kwargs`	`dict`	Style dict for QQ scatter (e.g., marker, s, edgecolor).	`{}`
`qq_xlabels`	`Any`	Custom x-axis tick labels for QQ plot.	required
`qq_xlim`	`Any`	X-axis limits for QQ plot, e.g., (min, max).	required
`qqscatterargs`	`Any`	QQ scatter kwargs alias.	required
`qtitle`	`Any`	Manhattan/QQ combined title.	required
`qtitle_pad`	`float`	QQ title padding.	`1.08`
`repel_force`	`float`	Text repulsion force parameter.	`0.03`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`sc_linewidth`	`int`	Line width for significance lines.	`2`
`scaled`	`bool`	Auto-detected when scaled effect columns exist; not a direct plot kwarg.	`False`
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size. Do not set in `scatter_kwargs`: edgecolor, edgecolors, linewidth, ax, palette, hue, data, legend, style, size, sizes, zorder, s.	required
`sig_line`	`bool`	Whether to draw significance reference line.	`True`
`sig_line_color`	`str or list`	Significance line color.	required
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`stratified`	`bool`	Enable stratified QQ by MAF.	`False`
`suggestive_sig_level`	`float`	Suggestive threshold value, e.g., 5e-6.	`5e-06`
`suggestive_sig_line`	`bool`	Whether to draw suggestive threshold line (e.g., 5e-6).	`False`
`suggestive_sig_line_color`	`str or list`	Suggestive significance line color.	required
`title`	`str`	Figure title text.	required
`title_fontsize`	`int`	Title font size.	`13`
`title_pad`	`float`	Title padding.	`1.08`
`use_rank`	`bool`	Use rank for chrom indexing.	`False`
`verbose`	`bool`	Verbose logging toggle.	`True`
`windowsizekb`	`int`	Window size for lead variant extraction (kb).	`500`
`xlabel`	`Any`	X-axis label.	required
`xpad`	`Any`	X padding proportion.	required
`xpadl`	`Any`	Left X padding.	required
`xpadr`	`Any`	Right X padding.	required
`xtick_chr_dict`	`Any`	X-axis tick chromosome mapping.	required
`xtight`	`bool`	Tight X padding.	`False`
`ylabel`	`Any`	Y-axis label.	required
`ylabels`	`Any`	Custom y-axis labels.	required
`ylim`	`Any`	Y-axis limits.	required
`ystep`	`int`	Step size for y-axis.	`0`
`ytick3`	`bool`	Use 3 y-axis ticks.	`True`

Returns:

Type	Description
`matplotlib.figure.Figure`	The created matplotlib figure object. tuple, optional `(lead_snp_is, lead_snp_is_color)` when `_get_region_lead=True` in regional mode.

Notes

- Regional plots require ``region=(chr, start, end)`` and LD data (``vcf_path`` or precomputed LD).
- Use ``skip`` to omit low-significance variants for faster genome-wide plots.
- Annotation supports gene names, custom columns, or variant IDs.

plot_manhattan

plot_manhattan(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Genome-wide Manhattan plot (mode='m').

Parameters:

Name	Type	Description	Default
`mode`	`str`	Plot layout mode. Values depend on the plot function; see ctx_desc.	`'mqq'`
`build`	`str`	Genome build (e.g., '19'/'38') for annotation/coordinate resources.	`None`
`sig_level`	`float`	Significance threshold for reference line and marker sizing.	`5e-08`
`anno_sig_level`	`float`	Significance level for extracting lead variants to annotate. Can be set independently from sig_level.	`5e-08`
`skip`	`int`	Minimum -log10(P) for variants shown on the plot (variants below this are omitted).	`0`
`cut`	`int`	Cap variant -log10(P) display above this value (squashes extreme peaks for layout).	`0`
`marker_size`	`list`	Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.	`[5, 20]`
`additional_line`	`Any`	Additional reference lines.	required
`additional_line_color`	`str or list`	Colors for additional lines.	required
`anno`	`DataFrame or list`	Annotation source or column (e.g., 'GENENAME', True, or column name).	required
`anno_adjust`	`bool`	Enable annotation position adjustment.	`False`
`anno_alias`	`dict`	Mapping from SNPID to custom annotation label.	`{}`
`anno_d`	`dict`	Per-annotation positioning options (e.g., left/right).	`{}`
`anno_fixed_arm_length`	`Any`	Fixed arm length for annotations.	required
`anno_fontsize`	`int`	Font size for annotation text.	`9`
`anno_gtf_path`	`str`	Custom GTF path for annotations.	required
`anno_height`	`int`	Height for annotations.	`1`
`anno_kwargs`	`dict`	Default styling kwargs for annotations.	`{}`
`anno_kwargs_single`	`dict`	Per-SNP styling kwargs for annotations.	`{}`
`anno_max_iter`	`int`	Maximum iterations for text repulsion algorithm.	`100`
`anno_max_rows`	`int`	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.	`40`
`anno_set`	`list`	Set of variant IDs to annotate.	`[]`
`anno_source`	`str`	Annotation source backend (e.g., 'ensembl', 'refseq').	`'ensembl'`
`anno_style`	`str`	Annotation style ('right', 'tight', 'expand').	`'right'`
`anno_xshift`	`Any`	X-axis shift applied to annotations.	required
`arm_offset`	`Any`	Offset for annotation arms.	required
`arm_scale`	`int`	Scaling factor for arm length.	`1`
`arm_scale_d`	`dict`	Per-annotation arm scaling dict.	`{}`
`arrow_kwargs`	`dict`	Arrow styling kwargs for annotations.	`{}`
`bwindowsizekb`	`int`	Window size in kilobases for density computation.	`100`
`check`	`bool`	Enable input QC and normalization.	`True`
`chr_dict`	`Any`	Chromosome number/name mapping.	required
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`chrpad`	`float`	Chromosome padding proportion.	`0.03`
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`cut_line_color`	`str or list`	Color for shrink line.	required
`cut_log`	`bool`	Use log scale for cut line.	`False`
`cutfactor`	`int`	Factor for shrink line.	`10`
`density_color`	`str or list`	Density palette or boolean to control density track colors.	required
`density_palette`	`str`	Density palette.	`'Reds'`
`density_range`	`Any`	Density value range.	required
`density_threshold`	`int`	Threshold for density highlighting.	`5`
`density_tpalette`	`str`	Palette for threshold coloring.	`'Blues'`
`density_trange`	`list`	Threshold range.	`[0, 10]`
`dpi`	`int`	Figure DPI.	`200`
`drop_chr_start`	`bool`	Drop chromosome start.	`False`
`ea`	`str`	Effect allele column.	`'EA'`
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`expected_min_mlog10p`	`int`	Expected minimum -log10(P) adjustment.	`0`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [15, 5], 'dpi': 200}`
`figax`	`Any`	Existing figure/axes tuple to draw on.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontfamily`	`str`	Font family alias.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`gc`	`bool`	Compute genomic control lambda.	`True`
`highlight`	`list`	List of focal variants to highlight.	`[]`
`highlight_anno_kwargs`	`dict`	Annotation style kwargs for highlighted variants.	`{}`
`highlight_chrpos`	`bool`	Highlight by chromosome position flag.	`False`
`highlight_color`	`str or list`	Highlight color.	required
`highlight_lim`	`Any`	Custom highlight limits.	required
`highlight_lim_mode`	`str`	Highlight limit mode ('absolute'\|'relative').	`'absolute'`
`highlight_windowkb`	`int`	Highlight window size (kb).	`500`
`include_chrXYMT`	`bool`	Include sex/MT chromosomes in QQ.	`True`
`jagged`	`bool`	Enable jagged axis break markers.	`False`
`jagged_len`	`float`	Jagged marker length.	`0.01`
`jagged_wid`	`float`	Jagged marker width.	`0.01`
`maf_bin_colors`	`str or list`	Colors for MAF bins.	required
`maf_bins`	`list`	MAF bin definitions for stratified QQ.	`[[0, 0.01], [0.01, 0.05], [0.05, 0.25], [0.25, 0.5]]`
`math_fontfamily`	`str`	Math text font family.	`'dejavusans'`
`mlog10p`	`str`	Negative log10 p-value column; improves performance and stability if provided.	`'MLOG10P'`
`mqqratio`	`int`	Layout ratio for combined Manhattan-QQ plot.	`3`
`mtitle`	`Any`	Manhattan title.	required
`mtitle_pad`	`float`	Manhattan title padding.	`1.08`
`nea`	`str`	Non-effect allele column.	`'NEA'`
`p`	`str`	P-value column.	`'P'`
`pinpoint`	`list`	Variants to pinpoint.	`[]`
`pinpoint_color`	`str or list`	Color for pinpoint.	required
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`qq_line_color`	`str or list`	Reference line color for QQ plot (e.g., 'grey').	required
`qq_scatter_kwargs`	`dict`	Style dict for QQ scatter (e.g., marker, s, edgecolor).	`{}`
`qq_xlabels`	`Any`	Custom x-axis tick labels for QQ plot.	required
`qq_xlim`	`Any`	X-axis limits for QQ plot, e.g., (min, max).	required
`qqscatterargs`	`Any`	QQ scatter kwargs alias.	required
`qtitle`	`Any`	Manhattan/QQ combined title.	required
`qtitle_pad`	`float`	QQ title padding.	`1.08`
`repel_force`	`float`	Text repulsion force parameter.	`0.03`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`sc_linewidth`	`int`	Line width for significance lines.	`2`
`scaled`	`bool`	Auto-detected when scaled effect columns exist; not a direct plot kwarg.	`False`
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size. Do not set in `scatter_kwargs`: edgecolor, edgecolors, linewidth, ax, palette, hue, data, legend, style, size, sizes, zorder, s.	required
`sig_line`	`bool`	Whether to draw significance reference line.	`True`
`sig_line_color`	`str or list`	Significance line color.	required
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`stratified`	`bool`	Enable stratified QQ by MAF.	`False`
`suggestive_sig_level`	`float`	Suggestive threshold value, e.g., 5e-6.	`5e-06`
`suggestive_sig_line`	`bool`	Whether to draw suggestive threshold line (e.g., 5e-6).	`False`
`suggestive_sig_line_color`	`str or list`	Suggestive significance line color.	required
`title`	`str`	Figure title text.	required
`title_fontsize`	`int`	Title font size.	`13`
`title_pad`	`float`	Title padding.	`1.08`
`use_rank`	`bool`	Use rank for chrom indexing.	`False`
`verbose`	`bool`	Verbose logging toggle.	`True`
`windowsizekb`	`int`	Window size for lead variant extraction (kb).	`500`
`xlabel`	`Any`	X-axis label.	required
`xpad`	`Any`	X padding proportion.	required
`xpadl`	`Any`	Left X padding.	required
`xpadr`	`Any`	Right X padding.	required
`xtick_chr_dict`	`Any`	X-axis tick chromosome mapping.	required
`xtight`	`bool`	Tight X padding.	`False`
`ylabel`	`Any`	Y-axis label.	required
`ylabels`	`Any`	Custom y-axis labels.	required
`ylim`	`Any`	Y-axis limits.	required
`ystep`	`int`	Step size for y-axis.	`0`
`ytick3`	`bool`	Use 3 y-axis ticks.	`True`

Returns:

Type	Description
`matplotlib.figure.Figure`	The created matplotlib figure object. tuple, optional `(lead_snp_is, lead_snp_is_color)` when `_get_region_lead=True` in regional mode.

Notes

- Regional plots require ``region=(chr, start, end)`` and LD data (``vcf_path`` or precomputed LD).
- Use ``skip`` to omit low-significance variants for faster genome-wide plots.
- Annotation supports gene names, custom columns, or variant IDs.

plot_snp_density

plot_snp_density(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Brisbane-style SNP density plot.

Parameters:

Name	Type	Description	Default
`mode`	`str`	Brisbane SNP-density layout (mode is forced to b).	`'mqq'`
`build`	`str`	Genome build (e.g., '19'/'38') for annotation/coordinate resources.	`None`
`sig_level`	`float`	Significance threshold for reference line and marker sizing.	`5e-08`
`anno_sig_level`	`float`	Significance level for extracting lead variants to annotate. Can be set independently from sig_level.	`5e-08`
`skip`	`int`	Minimum -log10(P) for variants shown on the plot (variants below this are omitted).	`0`
`cut`	`int`	Cap variant -log10(P) display above this value (squashes extreme peaks for layout).	`0`
`marker_size`	`list`	Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.	`[5, 20]`
`additional_line`	`Any`	Additional reference lines.	required
`additional_line_color`	`str or list`	Colors for additional lines.	required
`anno`	`DataFrame or list`	Annotation source or column (e.g., 'GENENAME', True, or column name).	required
`anno_adjust`	`bool`	Enable annotation position adjustment.	`False`
`anno_alias`	`dict`	Mapping from SNPID to custom annotation label.	`{}`
`anno_d`	`dict`	Per-annotation positioning options (e.g., left/right).	`{}`
`anno_fixed_arm_length`	`Any`	Fixed arm length for annotations.	required
`anno_fontsize`	`int`	Font size for annotation text.	`9`
`anno_gtf_path`	`str`	Custom GTF path for annotations.	required
`anno_height`	`int`	Height for annotations.	`1`
`anno_kwargs`	`dict`	Default styling kwargs for annotations.	`{}`
`anno_kwargs_single`	`dict`	Per-SNP styling kwargs for annotations.	`{}`
`anno_max_iter`	`int`	Maximum iterations for text repulsion algorithm.	`100`
`anno_max_rows`	`int`	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.	`40`
`anno_set`	`list`	Set of variant IDs to annotate.	`[]`
`anno_source`	`str`	Annotation source backend (e.g., 'ensembl', 'refseq').	`'ensembl'`
`anno_style`	`str`	Annotation style ('right', 'tight', 'expand').	`'right'`
`anno_xshift`	`Any`	X-axis shift applied to annotations.	required
`arm_offset`	`Any`	Offset for annotation arms.	required
`arm_scale`	`int`	Scaling factor for arm length.	`1`
`arm_scale_d`	`dict`	Per-annotation arm scaling dict.	`{}`
`arrow_kwargs`	`dict`	Arrow styling kwargs for annotations.	`{}`
`bwindowsizekb`	`int`	Window size in kilobases for density computation.	`100`
`check`	`bool`	Enable input QC and normalization.	`True`
`chr_dict`	`Any`	Chromosome number/name mapping.	required
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`chrpad`	`float`	Chromosome padding proportion.	`0.03`
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`cut_line_color`	`str or list`	Color for shrink line.	required
`cut_log`	`bool`	Use log scale for cut line.	`False`
`cutfactor`	`int`	Factor for shrink line.	`10`
`density_color`	`str or list`	Density palette or boolean to control density track colors.	required
`density_palette`	`str`	Density palette.	`'Reds'`
`density_range`	`Any`	Density value range.	required
`density_threshold`	`int`	Threshold for density highlighting.	`5`
`density_tpalette`	`str`	Palette for threshold coloring.	`'Blues'`
`density_trange`	`list`	Threshold range.	`[0, 10]`
`dpi`	`int`	Figure DPI.	`200`
`drop_chr_start`	`bool`	Drop chromosome start.	`False`
`ea`	`str`	Effect allele column.	`'EA'`
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`expected_min_mlog10p`	`int`	Expected minimum -log10(P) adjustment.	`0`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [15, 5], 'dpi': 200}`
`figax`	`Any`	Existing figure/axes tuple to draw on.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontfamily`	`str`	Font family alias.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`highlight`	`list`	List of focal variants to highlight.	`[]`
`highlight_anno_kwargs`	`dict`	Annotation style kwargs for highlighted variants.	`{}`
`highlight_chrpos`	`bool`	Highlight by chromosome position flag.	`False`
`highlight_color`	`str or list`	Highlight color.	required
`highlight_lim`	`Any`	Custom highlight limits.	required
`highlight_lim_mode`	`str`	Highlight limit mode ('absolute'\|'relative').	`'absolute'`
`highlight_windowkb`	`int`	Highlight window size (kb).	`500`
`include_chrXYMT`	`bool`	Include sex/MT chromosomes in QQ.	`True`
`jagged`	`bool`	Enable jagged axis break markers.	`False`
`jagged_len`	`float`	Jagged marker length.	`0.01`
`jagged_wid`	`float`	Jagged marker width.	`0.01`
`maf_bin_colors`	`str or list`	Colors for MAF bins.	required
`maf_bins`	`list`	MAF bin definitions for stratified QQ.	`[[0, 0.01], [0.01, 0.05], [0.05, 0.25], [0.25, 0.5]]`
`math_fontfamily`	`str`	Math text font family.	`'dejavusans'`
`mlog10p`	`str`	Negative log10 p-value column; improves performance and stability if provided.	`'MLOG10P'`
`mqqratio`	`int`	Layout ratio for combined Manhattan-QQ plot.	`3`
`mtitle`	`Any`	Manhattan title.	required
`mtitle_pad`	`float`	Manhattan title padding.	`1.08`
`nea`	`str`	Non-effect allele column.	`'NEA'`
`p`	`str`	P-value column.	`'P'`
`pinpoint`	`list`	Variants to pinpoint.	`[]`
`pinpoint_color`	`str or list`	Color for pinpoint.	required
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`qqscatterargs`	`Any`	QQ scatter kwargs alias.	required
`repel_force`	`float`	Text repulsion force parameter.	`0.03`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`sc_linewidth`	`int`	Line width for significance lines.	`2`
`scaled`	`bool`	Auto-detected when scaled effect columns exist; not a direct plot kwarg.	`False`
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size.	required
`sig_line`	`bool`	Whether to draw significance reference line.	`True`
`sig_line_color`	`str or list`	Significance line color.	required
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`suggestive_sig_level`	`float`	Suggestive threshold value, e.g., 5e-6.	`5e-06`
`suggestive_sig_line`	`bool`	Whether to draw suggestive threshold line (e.g., 5e-6).	`False`
`suggestive_sig_line_color`	`str or list`	Suggestive significance line color.	required
`title`	`str`	Figure title text.	required
`title_fontsize`	`int`	Title font size.	`13`
`title_pad`	`float`	Title padding.	`1.08`
`use_rank`	`bool`	Use rank for chrom indexing.	`False`
`verbose`	`bool`	Verbose logging toggle.	`True`
`windowsizekb`	`int`	Window size for lead variant extraction (kb).	`500`
`xlabel`	`Any`	X-axis label.	required
`xpad`	`Any`	X padding proportion.	required
`xpadl`	`Any`	Left X padding.	required
`xpadr`	`Any`	Right X padding.	required
`xtick_chr_dict`	`Any`	X-axis tick chromosome mapping.	required
`xtight`	`bool`	Tight X padding.	`False`
`ylabel`	`Any`	Y-axis label.	required
`ylabels`	`Any`	Custom y-axis labels.	required
`ylim`	`Any`	Y-axis limits.	required
`ystep`	`int`	Step size for y-axis.	`0`
`ytick3`	`bool`	Use 3 y-axis ticks.	`True`

Returns:

Type	Description
`matplotlib.figure.Figure`	The created matplotlib figure object. tuple, optional `(lead_snp_is, lead_snp_is_color)` when `_get_region_lead=True` in regional mode.

Notes

- Regional plots require ``region=(chr, start, end)`` and LD data (``vcf_path`` or precomputed LD).
- Use ``skip`` to omit low-significance variants for faster genome-wide plots.
- Annotation supports gene names, custom columns, or variant IDs.

plot_qq

plot_qq(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Quantile–quantile plot.

Parameters:

Name	Type	Description	Default
`skip`	`int`	Minimum -log10(P) for variants shown on the plot (variants below this are omitted).	`0`
`cut`	`int`	Cap variant -log10(P) display above this value (squashes extreme peaks for layout).	`0`
`marker_size`	`list`	Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.	required
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`cut_log`	`bool`	Use log scale for cut line.	`False`
`cutfactor`	`int`	Factor for shrink line.	`10`
`fig_kwargs`	`dict`	Figure kwargs for plot.	required
`figax`	`Any`	Existing figure/axes tuple to draw on.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`gc`	`bool`	Compute genomic control lambda.	`True`
`highlight`	`list`	List of focal variants to highlight.	`[]`
`mlog10p`	`str`	Observed -log10(P) used against expected under null in QQ plot.	`'MLOG10P'`
`p`	`str`	P-value column.	`'P'`
`pinpoint`	`list`	Variants to pinpoint.	`[]`
`qq_line_color`	`str or list`	Reference line color for QQ plot (e.g., 'grey').	required
`qq_scatter_kwargs`	`dict`	Style dict for QQ scatter (e.g., marker, s, edgecolor).	`{}`
`qq_xlabels`	`Any`	Custom x-axis tick labels for QQ plot.	required
`qq_xlim`	`Any`	X-axis limits for QQ plot, e.g., (min, max).	required
`qtitle`	`Any`	Manhattan/QQ combined title.	required
`qtitle_pad`	`float`	QQ title padding.	`1.08`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`title`	`str`	Figure title text.	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`ylabels`	`Any`	Custom y-axis labels.	required
`ystep`	`int`	Step size for y-axis.	`0`
`ytick3`	`bool`	Use 3 y-axis ticks.	`True`

Returns:

Type	Description
`matplotlib.figure.Figure`	The created matplotlib figure object. tuple, optional `(lead_snp_is, lead_snp_is_color)` when `_get_region_lead=True` in regional mode.

Notes

- Regional plots require ``region=(chr, start, end)`` and LD data (``vcf_path`` or precomputed LD).
- Use ``skip`` to omit low-significance variants for faster genome-wide plots.
- Annotation supports gene names, custom columns, or variant IDs.

plot_region

plot_region(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Regional association plot with optional LD, recombination, and gene tracks.

Parameters:

Name	Type	Description	Default
`mode`	`str`	Plot layout mode. Values depend on the plot function; see ctx_desc.	required
`region`	`tuple or str`	Required locus for plot_region(). Example: (7, 156538803, 157538803). Use get_region_start_and_end() to derive windows.	required
`build`	`str`	Genome build (e.g., '19'/'38') for annotation/coordinate resources.	`None`
`sig_level`	`float`	Significance threshold for reference line and marker sizing.	`5e-08`
`anno_sig_level`	`float`	Significance level for extracting lead variants to annotate. Can be set independently from sig_level.	`5e-08`
`skip`	`int`	Minimum -log10(P) for variants shown on the plot (variants below this are omitted).	`0`
`cut`	`int`	Cap variant -log10(P) display above this value (squashes extreme peaks for layout).	`0`
`marker_size`	`list`	Tuple (small, large) for non-lead vs lead/significant tiers on the locus scatter; reference overlay uses ~1.5× max.	`[40, 65]`
`vcf_path`	`str`	Required for LD-colored scatter, ld_block, and ld_link unless ld_path is provided. Biallelic unphased VCF is supported.	required
`ld_block`	`bool`	Requires vcf_path (or ld_path) and region. Controlled with ld_block_grid/anno_* options.	`False`
`ld_link`	`bool`	Draws pairs with r² ≥ region_ld_threshold[0]. Line color follows region_ld_colors bins (same as markers); alpha scales by r² × ld_link_alpha_scale. Filter pairs with ld_link_sig_level.	`False`
`additional_line`	`Any`	Additional reference lines.	required
`additional_line_color`	`str or list`	Colors for additional lines.	required
`anno`	`DataFrame or list`	Annotation source or column (e.g., 'GENENAME', True, or column name).	required
`anno_adjust`	`bool`	Enable annotation position adjustment.	`False`
`anno_alias`	`dict`	Mapping from SNPID to custom annotation label.	`{}`
`anno_cell`	`bool`	Used with ld_block=True; format via anno_cell_fmt.	`False`
`anno_cell_fmt`	`str`	Format string for LD cell annotations (e.g., '{:.2f}' for 2 decimal places).	`'{:.2f}'`
`anno_cell_kwargs`	`Any`	Additional keyword arguments for LD cell text annotations (e.g., {'fontsize': 10, 'weight': 'bold', 'color': 'white'}).	required
`anno_d`	`dict`	Per-annotation positioning options (e.g., left/right).	`{}`
`anno_fixed_arm_length`	`Any`	Fixed arm length for annotations.	required
`anno_fontsize`	`int`	Font size for annotation text.	`9`
`anno_gtf_path`	`str`	Custom GTF path for annotations.	required
`anno_height`	`int`	Height for annotations.	`1`
`anno_kwargs`	`dict`	Default styling kwargs for annotations.	`{}`
`anno_kwargs_single`	`dict`	Per-SNP styling kwargs for annotations.	`{}`
`anno_max_iter`	`int`	Maximum iterations for text repulsion algorithm.	`100`
`anno_max_rows`	`int`	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.	`40`
`anno_set`	`list`	Set of variant IDs to annotate.	`[]`
`anno_source`	`str`	Annotation source backend (e.g., 'ensembl', 'refseq').	`'ensembl'`
`anno_style`	`str`	Annotation style ('right', 'tight', 'expand').	`'right'`
`anno_xshift`	`Any`	X-axis shift applied to annotations.	required
`arm_offset`	`Any`	Offset for annotation arms.	required
`arm_scale`	`int`	Scaling factor for arm length.	`1`
`arm_scale_d`	`dict`	Per-annotation arm scaling dict.	`{}`
`arrow_kwargs`	`dict`	Arrow styling kwargs for annotations.	`{}`
`cbar_bbox_to_anchor`	`list`	Colorbar bbox_to_anchor.	`[0, 0, 1, 1]`
`cbar_borderpad`	`Any`	Colorbar border padding.	required
`cbar_downward_offset`	`float`	Colorbar downward offset.	`1.3`
`cbar_equal_aspect`	`bool`	Equal aspect for colorbar.	`True`
`cbar_font_family`	`str`	Colorbar font family.	`'Arial'`
`cbar_fontsize`	`int`	Colorbar font size.	`12`
`cbar_h_scale`	`int`	Colorbar height scale.	`1`
`cbar_scale`	`bool`	Scale colorbar.	`True`
`cbar_title`	`str`	Shown when region_ld_legend=True; LaTeX r² supported in default.	`'LD $\\mathregular{r^2}$ with variant'`
`cbar_w_scale`	`int`	Colorbar width scale.	`1`
`check`	`bool`	Enable input QC and normalization.	`True`
`chr_dict`	`Any`	Chromosome number/name mapping.	required
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`chrpad`	`float`	Chromosome padding proportion.	`0.03`
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`cut_line_color`	`str or list`	Color for shrink line.	required
`cut_log`	`bool`	Use log scale for cut line.	`False`
`cutfactor`	`int`	Factor for shrink line.	`10`
`dpi`	`int`	Figure DPI.	`200`
`drop_chr_start`	`bool`	Drop chromosome start.	`False`
`ea`	`str`	Effect allele column.	`'EA'`
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [15, 15], 'dpi': 200}`
`figax`	`Any`	Existing figure/axes tuple to draw on.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontfamily`	`str`	Font family alias.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`gtf_chr_dict`	`Any`	GTF chromosome dictionary.	required
`gtf_gene_name`	`Any`	GTF gene name column.	required
`gtf_path`	`str`	'default' uses built-in annotation for build. Filter protein-coding with region_protein_coding.	`'default'`
`ld_block_anno`	`bool`	Left-side variant labels on the LD triangle; True uses chr:pos, or pass a column name (SNPID, rsID).	`False`
`ld_block_anno_kwargs`	`Any`	Additional keyword arguments for left-side annotations (e.g., {'fontsize': 8, 'color': 'black'}).	required
`ld_block_anno_max_rows`	`int`	Maximum number of variants to annotate. If the number of variants to annotate exceeds this limit, annotations will be skipped.	`100`
`ld_block_anno_set`	`Any`	List of SNPIDs to annotate. If None, annotates all variants. Variants are matched by SNPID column.	required
`ld_block_grid`	`bool`	Style via ld_block_grid_kwargs; panel requires ld_block=True.	`False`
`ld_block_grid_kwargs`	`Any`	Additional keyword arguments for LD block grid lines (e.g., {'color': 'gray', 'linewidth': 0.5, 'alpha': 0.5}).	required
`ld_fmt`	`str`	LD format identifier (e.g., 'npz').	`'npz'`
`ld_if_add_T`	`bool`	Add transpose when composing LD.	`False`
`ld_if_square`	`bool`	Treat LD matrix as square.	`False`
`ld_link_alpha_scale`	`float`	Higher values make high-LD links more opaque.	`0.2`
`ld_link_color`	`str or list`	Currently unused—line colors match region_ld_threshold/region_ld_colors bins.	required
`ld_link_linewidth`	`float`	Fixed width; color/alpha still reflect LD bin and r².	`1.0`
`ld_link_sig_level`	`Any`	Defaults to sig_level when None. Independent from anno_sig_level.	required
`ld_link_thr`	`float`	Currently not read by the implementation—minimum link r² is region_ld_threshold[0]; set bins via region_ld_threshold instead.	`0.8`
`ld_map_kwargs`	`Any`	Extra kwargs for LD map loader.	required
`ld_map_path`	`str`	Path to LD map file.	required
`ld_map_rename_dic`	`Any`	Rename dictionary for LD map columns.	required
`ld_path`	`str`	When set with ld_fmt, skips VCF LD calculation.	required
`math_fontfamily`	`str`	Math text font family.	`'dejavusans'`
`mlog10p`	`str`	-log10(P) values for y-axis in regional plot.	`'MLOG10P'`
`nea`	`str`	Non-effect allele column.	`'NEA'`
`p`	`str`	P-value column.	`'P'`
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`qqscatterargs`	`Any`	QQ scatter kwargs alias.	required
`region_anno_bbox_kwargs`	`dict`	Annotation bbox kwargs for region.	`{'ec': 'None', 'fc': 'None'}`
`region_flank_factor`	`float`	Expands (start, end) symmetrically before plotting.	`0.05`
`region_grid`	`bool`	Styled with region_grid_line.	`False`
`region_grid_line`	`dict`	Grid line style for regional plot.	`{'linewidth': 2, 'linestyle': '--'}`
`region_hspace`	`float`	Matplotlib hspace between ax1/ax3/ax4 panels.	`0.02`
`region_ld_colors`	`str or list`	List length = len(region_ld_threshold)+3. Index 0: no/missing LD; indices 1…N: LD intervals between thresholds; last index: reference/lead variant. Default 7 colors for 4 thresholds. ld_link reuses these colors.	required
`region_ld_colors_m`	`list`	When len(region_ref)>1, each color builds a white→color gradient across the same bins as region_ld_threshold. Variant shape comes from region_marker_shapes[1+] per reference, not from LD tier.	`['#E51819', '#367EB7', 'green', '#F07818', '#AD5691', 'yellow', 'purple']`
`region_ld_legend`	`bool`	True when vcf_path or ld_path supplies LD; uses region_ld_threshold/colors legend.	`True`
`region_ld_threshold`	`list`	Ascending r² boundaries, e.g. [0.2, 0.4, 0.6, 0.8]. Bins: missing/0, (0→t0], (t0→t1], …, (t_last→1], plus reference/lead. Pair with region_ld_colors (len = len(thresholds)+3). ld_link draws pairs with r² ≥ thresholds[0].	`[0.2, 0.4, 0.6, 0.8]`
`region_lead_grid`	`bool`	Styled with region_lead_grid_line (default red dashed).	`True`
`region_lead_grid_line`	`dict`	Default: red dashed, alpha 0.5, linewidth 2. Used when region_lead_grid=True.	`{'alpha': 0.5, 'linewidth': 2, 'linestyle': '--', 'color': '#FF0000'}`
`region_legend_marker`	`bool`	Uses region_marker_shapes[2] (single-ref) inside the colorbar when True.	`True`
`region_marker_shapes`	`list`	Shape by index; LD r² 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)—single-ref uses index 2; multi-ref uses 2, 3, … Do not set scatter_kwargs['marker'].	`['X', 'o', '^', 's', 'D', '*', 'P', 'h', '8']`
`region_protein_coding`	`bool`	Applies when gtf_path is set (or 'default').	`True`
`region_recombination`	`bool`	Uses rr_path, rr_lim, rr_ylabel; disable to hide the RR panel.	`True`
`region_ref`	`Any`	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.	required
`region_ref_alias`	`Any`	Dict {variant_id: label} for colorbar/legend text.	required
`region_ref_second`	`Any`	Deprecated pattern—include all references in region_ref instead.	required
`region_step`	`int`	Default 21 tick steps across the plotted window.	`21`
`region_title`	`Any`	None auto-builds from region and lead variant; pass through region_title_args/kwargs.	required
`region_title_kwargs`	`dict`	Regional plot title styling args.	`{'family': 'Arial'}`
`repel_force`	`float`	Text repulsion force parameter.	`0.03`
`rr_chr_dict`	`Any`	Recombination rate chrom dict.	required
`rr_header_dict`	`Any`	Recombination rate header dict.	required
`rr_lim`	`list`	Tuple (min, max); default (0, 100).	`[0, 100]`
`rr_path`	`str`	Used when region_recombination=True; y-axis limits from rr_lim.	`'default'`
`rr_ylabel`	`bool`	Applies to the RR panel when region_recombination=True.	`True`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`sc_linewidth`	`int`	Line width for significance lines.	`2`
`scaled`	`bool`	Auto-detected when scaled effect columns exist; not a direct plot kwarg.	`False`
`scatter_kwargs`	`dict`	Extra kwargs for locus scatter points. Do not set 's' (use marker_size) or 'marker' (use region_marker_shapes). Do not set in `scatter_kwargs`: edgecolor, edgecolors, linewidth, ax, palette, hue, data, legend, style, size, sizes, zorder, s.	required
`show_ld_score`	`bool`	LD score = sum of r² to other variants; requires vcf_path or ld_path.	`False`
`sig_line`	`bool`	Whether to draw significance reference line.	`True`
`sig_line_color`	`str or list`	Significance line color.	required
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`suggestive_sig_level`	`float`	Suggestive threshold value, e.g., 5e-6.	`5e-06`
`suggestive_sig_line`	`bool`	Whether to draw suggestive threshold line (e.g., 5e-6).	`False`
`suggestive_sig_line_color`	`str or list`	Suggestive significance line color.	required
`tabix`	`Any`	Tabix index path for fast IO.	required
`taf`	`list`	Track arrangement factors.	`[4, 0, 0.95, 1, 1]`
`title`	`str`	Figure title text.	required
`title_fontsize`	`int`	Title font size.	`13`
`title_pad`	`float`	Title padding.	`1.08`
`track_exon_ratio`	`int`	Exon track ratio.	`1`
`track_font_family`	`str`	Font family for region tracks.	`'Arial'`
`track_fontsize_ratio`	`float`	Track fontsize ratio.	`0.95`
`track_n`	`int`	Genes beyond this limit are omitted; adjust track_n_offset for spacing.	`4`
`track_n_offset`	`int`	Track offset.	`0`
`track_text_offset`	`int`	Track text offset.	`1`
`use_rank`	`bool`	Use rank for chrom indexing.	`False`
`vcf_chr_dict`	`Any`	Chromosome mapping for VCF resource.	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`windowsizekb`	`int`	Window size for lead variant extraction (kb).	`500`
`xlabel`	`Any`	X-axis label.	required
`xpad`	`Any`	X padding proportion.	required
`xpadl`	`Any`	Left X padding.	required
`xpadr`	`Any`	Right X padding.	required
`xtick_chr_dict`	`Any`	X-axis tick chromosome mapping.	required
`xtight`	`bool`	Tight X padding.	`False`
`ylabel`	`Any`	Y-axis label.	required
`ylabels`	`Any`	Custom y-axis labels.	required
`ylim`	`Any`	Y-axis limits.	required
`ystep`	`int`	Step size for y-axis.	`0`
`ytick3`	`bool`	Use 3 y-axis ticks.	`True`

Returns:

Type	Description
`matplotlib.figure.Figure`	The created matplotlib figure object. tuple, optional `(lead_snp_is, lead_snp_is_color)` when `_get_region_lead=True` in regional mode.

Notes

- Regional plots require ``region=(chr, start, end)`` and LD data (``vcf_path`` or precomputed LD).
- Use ``skip`` to omit low-significance variants for faster genome-wide plots.
- Annotation supports gene names, custom columns, or variant IDs.

plot_trumpet

plot_trumpet(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Trumpet plot for quantitative (mode='q') or binary (mode='b') traits. Binary-only parameters: prevalence, ncase, ncontrol, or_to_rr.

Parameters:

Name	Type	Description	Default
`mode`	`str`	Plot layout mode. Values depend on the plot function; see ctx_desc.	`'q'`
`build`	`str`	Genome build (e.g., '19'/'38') for annotation/coordinate resources.	`None`
`sig_level`	`float`	Significance threshold for reference line and marker sizing.	`5e-08`
`anno`	`DataFrame or list`	Annotation source or column (e.g., 'GENENAME', True, or column name).	required
`anno_alias`	`dict`	Mapping from SNPID to custom annotation label.	`{}`
`anno_d`	`dict`	Per-annotation positioning options (e.g., left/right).	`{}`
`anno_kwargs`	`dict`	Default styling kwargs for annotations.	`{}`
`anno_max_iter`	`int`	Maximum iterations for text repulsion algorithm.	`100`
`anno_set`	`list`	Set of variant IDs to annotate.	`[]`
`anno_source`	`str`	Annotation source backend (e.g., 'ensembl', 'refseq').	`'ensembl'`
`anno_style`	`str`	Annotation style ('right', 'tight', 'expand').	`'right'`
`anno_x`	`float`	Annotation x threshold.	`0.01`
`anno_y`	`int`	Annotation y threshold.	`1`
`arm_scale`	`int`	Scaling factor for arm length.	`1`
`beta`	`str`	Effect size column.	`'BETA'`
`beta_range`	`Any`	Beta range for power computation.	required
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`cmap`	`Any`	Colormap selection.	required
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`highlight`	`list`	List of focal variants to highlight.	`[]`
`highlight_anno_kwargs`	`dict`	Annotation style kwargs for highlighted variants.	`{}`
`highlight_chrpos`	`bool`	Highlight by chromosome position flag.	`False`
`highlight_color`	`str or list`	Highlight color.	required
`highlight_lim`	`Any`	Custom highlight limits.	required
`highlight_lim_mode`	`str`	Highlight limit mode ('absolute'\|'relative').	`'absolute'`
`highlight_windowkb`	`int`	Highlight window size (kb).	`500`
`hue`	`Any`	Hue mapping.	required
`maf`	`str`	Minor allele frequency column.	`'MAF'`
`maf_range`	`Any`	MAF range for power computation.	required
`markercolor`	`str`	Base marker color.	`'#597FBD'`
`n`	`Any`	Sample size column (quantitative mode).	required
`n_matrix`	`int`	Power curve smoothness parameter.	`1000`
`ncase`	`Any`	Case count (binary mode).	required
`ncontrol`	`Any`	Control count (binary mode).	required
`or_to_rr`	`bool`	Convert OR to RR.	`False`
`p`	`str`	P-value column.	`'P'`
`p_level`	`float`	P-value threshold for inclusion.	`5e-08`
`pinpoint`	`list`	Variants to pinpoint.	`[]`
`pinpoint_color`	`str or list`	Color for pinpoint.	required
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`prevalence`	`Any`	Disease prevalence (used for power lines in binary mode).	required
`repel_force`	`float`	Text repulsion force parameter.	`0.03`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size.	required
`size`	`Any`	Size mapping.	required
`sizes`	`Any`	Size list for style mapping.	required
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`sort`	`Any`	Sorting key or method.	required
`title`	`str`	Figure title text.	required
`title_fontsize`	`int`	Title font size.	`13`
`ts`	`Any`	Power thresholds to plot.	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`xlabel`	`Any`	X-axis label.	required
`xlim`	`Any`	X-axis limits.	required
`xscale`	`str`	X-axis scale.	`'log'`
`xticklabels`	`Any`	Custom x-axis tick labels.	required
`xticks`	`Any`	Custom x-axis ticks.	required
`ylabel`	`Any`	Y-axis label.	required
`ylim`	`Any`	Y-axis limits.	required
`yscale_factor`	`int`	Y scale factor.	`1`
`yticklabels`	`Any`	Custom y-axis tick labels.	required
`yticks`	`Any`	Custom y-axis ticks.	required

Returns:

Type	Description
`matplotlib.figure.Figure`	The generated trumpet plot figure.

plot_phenogram

plot_phenogram(build: Optional[str] = None, **kwargs: Any) -> typing.Any

Create a karyotype-style phenogram with cytobands and lead variants.

Registry-aligned parameters are on ``Sumstats.plot_phenogram()``.

Returns:

Type	Description
`Figure`	The phenogram figure.

Parameters:

Name	Type	Description	Default
`build`	`str`	Genome build (e.g., '19'/'38') for annotation/coordinate resources.	`'19'`
`sig_level`	`float`	Significance threshold for reference line and marker sizing.	`5e-08`
`anno_sig_level`	`float`	Significance level for extracting lead variants to annotate. Can be set independently from sig_level.	`5e-08`
`marker_size`	`int`	Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.	`81`
`anno`	`DataFrame or list`	Annotation source or column (e.g., 'GENENAME', True, or column name).	required
`anno_alias`	`dict`	Mapping from SNPID to custom annotation label.	`{}`
`anno_color`	`str or list`	Column name for phenogram marker color; unique values auto-mapped to marker_colors pool.	required
`anno_group`	`Any`	Column name to merge multiple phenogram leads into one label.	required
`anno_gtf_path`	`str`	Custom GTF path for annotations.	required
`anno_kwargs`	`dict`	Default styling kwargs for annotations.	`{}`
`anno_kwargs_single`	`dict`	Per-SNP styling kwargs for annotations.	`{}`
`anno_max_iter`	`int`	Maximum iterations for text repulsion algorithm.	`100`
`anno_max_len`	`Any`	Truncate phenogram annotation labels to this length.	required
`anno_max_rows`	`int`	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.	`200`
`anno_set`	`list`	Set of variant IDs to annotate.	`[]`
`anno_shape`	`Any`	Column name for phenogram marker shape; unique values auto-mapped to marker_shapes pool.	required
`anno_source`	`str`	Annotation source backend (e.g., 'ensembl', 'refseq').	`'ensembl'`
`anno_style`	`str`	Annotation style ('right', 'tight', 'expand').	`'expand'`
`anno_wrap`	`Any`	Enable text wrapping for phenogram annotations.	required
`anno_wrap_chars_per_line`	`Any`	Character wrap width for phenogram annotations.	required
`anno_wrap_width_pt`	`Any`	Max annotation line width in points (phenogram).	required
`anno_x_pad`	`float`	Phenogram extra horizontal gap between chromosome and annotation text (data coords).	`0.18`
`arrow_kwargs`	`dict`	Arrow styling kwargs for annotations.	`{}`
`chr_label_pad`	`float`	chr_label_pad.	`0.06`
`chr_width`	`float`	Phenogram chromosome width in data coordinates.	`0.35`
`chr_x`	`float`	Phenogram chromosome left x boundary in data coordinates.	`0.0`
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`cytoband_path`	`str`	cytoband_path.	required
`dpi`	`int`	Figure DPI.	`100`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [15, 15], 'dpi': 200}`
`figsize`	`list`	figsize.	`[20, 48]`
`group_label_box_pad_pt`	`float`	Extra padding around phenogram label text for overlap calculations, in points.	`1.5`
`group_marker_to_marker_gap_pt`	`int`	Minimum spacing between marker rows of adjacent phenogram groups, in points.	`3`
`group_min_vertical_gap_pt`	`float`	Minimum vertical spacing between phenogram group annotation blocks, in points.	`3.5`
`include_sex_chr`	`bool`	If True, include chrX and chrY after autosomes in phenogram.	`False`
`legend_kwargs`	`dict`	Legend styling kwargs.	`{}`
`legend_ncol`	`int`	Number of columns in phenogram figure legend.	`6`
`marker_color_map`	`Any`	Map from phenogram anno_color values to marker colors.	required
`marker_colors`	`str or list`	Pool of colors for auto phenogram color mapping.	required
`marker_fontsize`	`int`	Font size for phenogram marker-mode text labels.	`11`
`marker_gap_pt`	`int`	Horizontal gap between phenogram markers within a group, in points.	`3`
`marker_label_align`	`str`	Horizontal alignment of phenogram marker label relative to marker row (center, left, right).	`'center'`
`marker_label_bbox`	`bool`	If True, draw phenogram marker labels with a white text outline (no filled box).	`True`
`marker_label_gap_pt`	`float`	Vertical gap between phenogram marker row and text label below, in points.	`2.75`
`marker_linewidth`	`float`	Edge linewidth for phenogram marker scatter points.	`0.6`
`marker_max_per_row`	`int`	marker_max_per_row.	`4`
`marker_row_gap_pt`	`float`	marker_row_gap_pt.	`2.5`
`marker_shape_map`	`Any`	Map from phenogram anno_shape values to matplotlib marker codes.	required
`marker_shapes`	`Any`	Pool of matplotlib marker codes for auto phenogram shape mapping.	required
`mlog10p`	`str`	Negative log10 p-value column; improves performance and stability if provided.	`'MLOG10P'`
`ncols`	`int`	ncols.	`11`
`only_anno_chr`	`bool`	If True, plot only chromosomes containing phenogram lead or annotation rows.	`False`
`p`	`str`	P-value column.	`'P'`
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`repel_force`	`float`	Text repulsion force parameter.	`0.03`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	`False`
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`show_legend`	`bool`	Show figure-level legend below phenogram.	`True`
`snpid`	`str`	SNP identifier column.	`'SNPID'`
`use_lead_extraction`	`bool`	If True, extract lead variants via _get_sig(); if False, use every input row.	`True`
`verbose`	`bool`	Verbose logging toggle.	`True`
`windowsizekb`	`int`	Window size for lead variant extraction (kb).	`500`

Returns:

Type	Description
`matplotlib.figure.Figure`	The phenogram figure.

plot_ld_block

plot_ld_block(**kwargs: Any) -> typing.Any

Plot the upper triangle of an LD matrix as a 45°-rotated inverted triangle.

This function supports two modes:
1. **Standalone mode**: Creates its own figure and plots LD block independently.
2. **Regional mode**: Plots on provided axes (typically from plot_mqq) and aligns
   x-axis with regional plot using "i" coordinate system.

Returns:

Name	Type	Description
`fig`	`Figure`	Figure object.
`ax`	`Axes`	Axes object.

Parameters:

Name	Type	Description	Default
`mode`	`str`	Plot layout mode. Values depend on the plot function; see ctx_desc.	required
`region`	`tuple or str`	Genomic locus as (chr, start, end) in base pairs.	required
`vcf_path`	`str`	Reference-panel VCF for LD r² computation.	required
`anno_cell`	`bool`	Annotate LD block matrix cells with r² values.	`False`
`anno_cell_fmt`	`str`	Format string for LD cell annotations (e.g., '{:.2f}' for 2 decimal places).	`'{:.2f}'`
`anno_cell_kwargs`	`Any`	Additional keyword arguments for LD cell text annotations (e.g., {'fontsize': 10, 'weight': 'bold', 'color': 'white'}).	required
`ax`	`Any`	ax.	required
`ax_pos`	`Any`	ax_pos.	required
`cbar`	`bool`	cbar.	`True`
`cbar_kwargs`	`Any`	cbar_kwargs.	required
`cbar_label`	`str`	cbar_label.	`'LD $\\mathregular{r^2}$ with variant'`
`cmap`	`Any`	Colormap selection.	required
`ea_col`	`str`	ea_col.	`'EA'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`10`
`ld`	`Any`	ld.	required
`ld_block_anno`	`bool`	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.	`False`
`ld_block_anno_kwargs`	`Any`	Additional keyword arguments for left-side annotations (e.g., {'fontsize': 8, 'color': 'black'}).	required
`ld_block_anno_max_rows`	`int`	Maximum number of variants to annotate. If the number of variants to annotate exceeds this limit, annotations will be skipped.	`100`
`ld_block_anno_set`	`Any`	List of SNPIDs to annotate. If None, annotates all variants. Variants are matched by SNPID column.	required
`ld_block_grid`	`bool`	Draw grid lines on the LD matrix triangle panel.	`False`
`ld_block_grid_kwargs`	`Any`	Additional keyword arguments for LD block grid lines (e.g., {'color': 'gray', 'linewidth': 0.5, 'alpha': 0.5}).	required
`lead_snp_is`	`Any`	lead_snp_is.	required
`lead_snp_is_color`	`str or list`	lead_snp_is_color.	required
`mapper`	`Any`	mapper.	required
`nea_col`	`str`	nea_col.	`'NEA'`
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`pos_col`	`str`	pos_col.	`'POS'`
`position_bar_bg`	`bool`	position_bar_bg.	`True`
`region_step`	`int`	Number of major tick intervals on the locus x-axis.	`21`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`sumstats`	`Any`	Sumstats or DataFrame for LD block when using vcf_path+region.	required
`tabix`	`Any`	Tabix index path for fast IO.	required
`title`	`str`	Figure title text.	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`vmax`	`float`	vmax.	`1.0`
`vmin`	`float`	vmin.	`0.0`
`xlabel`	`str`	X-axis label.	`'Genomic position'`

Returns:

Type	Description
`matplotlib.figure.Figure`	Figure object. matplotlib.axes.Axes Axes object.

plot_effect

plot_effect(**kwargs: Any) -> None

Plot effect sizes with optional EAF and SNPR2 side panels.

Registry-aligned parameters are on ``Sumstats.plot_effect()``.

Returns:

Type	Description
`Figure`	The generated figure object.

Parameters:

Name	Type	Description	Default
`eaf`	`str`	Effect allele frequency column.	`'EAF'`
`eaf_kwargs`	`dict`	Styling kwargs for EAF panel.	`{}`
`eaf_label`	`Any`	Label for EAF panel.	required
`eaf_panel`	`Any`	Toggle EAF panel.	required
`effect_label`	`Any`	Label for effect size panel.	required
`err_kwargs`	`dict`	Errorbar styling kwargs.	`{'ecolor': '#cccccc', 'linewidth': 0, 'zorder': 90, 'elinewidth': 1}`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [8, 8], 'dpi': 200}`
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`font_kwargs`	`dict`	Font configuration kwargs.	`{'fontsize': 9}`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`gap`	`float`	Panel gap or spacing.	`0.3`
`group`	`Any`	Grouping column for axes.	required
`hue`	`Any`	Hue mapping.	required
`legend_mode`	`int`	Legend layout: int code (plot_effect) or string mode (compare_effect).	`1`
`ncol`	`int`	Number of columns in legend.	`2`
`rename_dic`	`Any`	Rename dictionary for labels.	required
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size.	`{'s': 20}`
`se`	`str`	Standard error column.	`'SE'`
`size`	`Any`	Size mapping.	required
`snpr2`	`Any`	SNP r2 column.	required
`snpr2_kwargs`	`dict`	Styling kwargs for SNP r2 panel.	`{'color': '#74BAD3'}`
`snpr2_label`	`Any`	Label for SNP r2 panel.	required
`snpvar_panel`	`Any`	Toggle SNP variance panel.	required
`sort_kwargs`	`Any`	Sorting kwargs.	required
`style_col`	`Any`	style_col.	required
`title`	`str`	Figure title text.	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`x`	`Any`	X variable/column name.	required
`xlim_eaf`	`Any`	X limits for EAF panel.	required
`xlim_snpr2`	`Any`	X limits for SNP r2 panel.	required
`y`	`Any`	Y variable/column name.	required
`y_sort`	`Any`	Y sorting key.	required
`ylabel`	`Any`	Y-axis label.	required

Returns:

Type	Description
`matplotlib.figure.Figure`	The generated figure object.

plot_associations

plot_associations(**kwargs)

Plot trait associations as a heatmap (GCV2 format).

Parameters:

Name	Type	Description	Default
`annot`	`bool`	annot.	`True`
`cbar`	`bool`	cbar.	`True`
`cbar_kws`	`Any`	cbar_kws.	required
`center`	`Any`	center.	required
`cmap`	`str`	Colormap selection.	`'RdBu'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	required
`fmt`	`str`	fmt.	`'.2f'`
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`heatmap_kwargs`	`Any`	heatmap_kwargs.	required
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`sort`	`str`	Sorting key or method.	`'P_GCV2'`
`title`	`str`	Figure title text.	required
`values`	`str`	Value to plot in associations heatmap.	`'Beta'`
`verbose`	`bool`	Verbose logging toggle.	`True`
`vmax`	`Any`	vmax.	required
`vmin`	`Any`	vmin.	required
`xlabel`	`str`	X-axis label.	`'rsID - Gene Name'`
`xticklabel_kwargs`	`dict`	X ticklabel kwargs.	`{'rotation': 45, 'horizontalalignment': 'left', 'verticalalignment': 'bottom', 'fontsize': 10, 'fontfamily': 'Arial'}`
`ylabel`	`str`	Y-axis label.	`'Traits'`
`yticklabel_kwargs`	`dict`	Matplotlib kwargs for LDSC rg heatmap y-axis tick labels (rotation, fontsize, …).	`{'fontsize': 10, 'fontfamily': 'Arial'}`

Returns:

Type	Description
`matplotlib.figure.Figure or None`	Heatmap figure, or `None` when required columns are missing. matplotlib.axes.Axes or None Axes containing the heatmap.

plot_sankey

plot_sankey(**kwargs: Any) -> typing.Any

Sankey diagram across ordered categorical stages. Pass stage names via columns (list of column or preset names).

Parameters:

Name	Type	Description	Default
`beta_bins`	`Any`	beta_bins.	required
`color_by`	`str`	color_by.	`'first'`
`colors`	`list`	Color palette or list.	`['#597FBD', '#74BAD3']`
`column_map`	`Any`	column_map.	required
`dropna`	`bool`	dropna.	`True`
`fig_kwargs`	`dict`	Figure kwargs for plot.	`{'figsize': [10, 6], 'dpi': 300}`
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`gap_frac`	`float`	gap_frac.	`0.02`
`link_alpha`	`float`	link_alpha.	`0.55`
`node_color_mode`	`str`	node_color_mode.	`'stacked'`
`node_width`	`float`	node_width.	`0.025`
`palette`	`str`	Color palette name or list.	`'auto'`
`ribbon_curvature`	`float`	ribbon_curvature.	`0.5`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	`False`
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	`{'dpi': 300, 'facecolor': 'white'}`
`stage_labels`	`Any`	stage_labels.	required
`title`	`str`	Figure title text.	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`weight`	`str`	weight.	`'count'`

Returns:

Type	Description
`tuple`	`(fig, ax, tables)` where `tables` contains `nodes`, `links`, `node_bands`, `flow_colors`, `stages`, and `work`. Returns `(None, None, tables)` when no rows remain after filtering.

plot_pipcs

plot_pipcs(region=None, locus=None, **kwargs)

Plot fine-mapping credible sets in a regional view.

Parameters:

Name	Type	Description	Default
`region`	`tuple or str`	Genomic locus as (chr, start, end) in base pairs.	`None`
`marker_size`	`int`	Scatter marker size. Use an int for fixed size, or a (small, large) tuple for variants below/above sig_level.	`40`
`chrom`	`str`	Chromosome column used to position variants and x-axis layout.	`'CHR'`
`cs`	`str`	Credible-set index column.	`'CREDIBLE_SET_INDEX'`
`cs_category`	`str`	Column name for credible-set category label.	`'CS_CATEGORY'`
`fig_kwargs`	`dict`	Figure kwargs for plot.	required
`figax`	`Any`	Existing figure/axes tuple to draw on.	required
`font_family`	`str`	Font family, e.g., 'Arial', for consistent styling.	`'Arial'`
`fontsize`	`int`	Font size for ticks, labels, etc.	`12`
`legend_title`	`Any`	Legend title.	required
`locus`	`Any`	Locus label for credible sets.	`None`
`onlycs`	`bool`	When True, plot only CS-assigned variants.	`False`
`pip`	`str`	PIP column in finemapping results.	`'PIP'`
`pos`	`str`	Base-pair position column used with `chrom` for plotting.	`'POS'`
`save`	`bool`	Boolean or output filepath; when boolean, uses default naming.	required
`save_kwargs`	`dict`	Save kwargs for GW heatmap.	required
`scatter_kwargs`	`dict`	Extra kwargs passed to the main scatter layer (matplotlib Axes.scatter). Use marker_size for point sizes, not s/size.	required
`title`	`str`	Figure title text.	required
`title_kwargs`	`Any`	Title styling kwargs (e.g., family, fontsize, weight).	required
`verbose`	`bool`	Verbose logging toggle.	`True`
`xtick_chr_dict`	`Any`	X-axis tick chromosome mapping.	required

Returns:

Type	Description
`matplotlib.figure.Figure`	The credible-set regional figure.