plot-io 0.12.0__py3-none-win_arm64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- plot_io/__init__.py +73 -0
- plot_io/_methods.py +1691 -0
- plot_io/_native/__init__.py +199 -0
- plot_io/_native/__main__.py +197 -0
- plot_io/_native/_api.py +457 -0
- plot_io/_native/bin/windows-arm64.dll +0 -0
- plot_io/_native/kernels.py +335 -0
- plot_io/_native/manifest.json +49 -0
- plot_io/axis.py +1347 -0
- plot_io/boxes.py +1156 -0
- plot_io/canvas.py +389 -0
- plot_io/color/__init__.py +3 -0
- plot_io/color/data.py +1646 -0
- plot_io/color/maps.py +922 -0
- plot_io/color/values.py +295 -0
- plot_io/color/variants.py +1246 -0
- plot_io/colorbar.py +1426 -0
- plot_io/columns.py +614 -0
- plot_io/decorations.py +920 -0
- plot_io/defaults.py +809 -0
- plot_io/density.py +113 -0
- plot_io/ext.py +68 -0
- plot_io/facets.py +240 -0
- plot_io/figure.py +788 -0
- plot_io/formatters.py +97 -0
- plot_io/genome/__init__.py +17 -0
- plot_io/genome/adapters.py +356 -0
- plot_io/genome/combine.py +123 -0
- plot_io/genome/contacts.py +508 -0
- plot_io/genome/intervals.py +750 -0
- plot_io/genome/lanes.py +191 -0
- plot_io/genome/layout.py +184 -0
- plot_io/genome/links.py +364 -0
- plot_io/genome/pack.py +27 -0
- plot_io/genome/readers.py +145 -0
- plot_io/genome/regions.py +228 -0
- plot_io/genome/scale.py +349 -0
- plot_io/genome/series.py +344 -0
- plot_io/genome/signal.py +621 -0
- plot_io/genome/sites.py +782 -0
- plot_io/genome/sources.py +459 -0
- plot_io/genome/testing.py +161 -0
- plot_io/geometry.py +289 -0
- plot_io/groups.py +308 -0
- plot_io/guides.py +503 -0
- plot_io/helpers/__init__.py +17 -0
- plot_io/helpers/clustermap.py +202 -0
- plot_io/helpers/dendrogram.py +172 -0
- plot_io/helpers/grids.py +304 -0
- plot_io/helpers/qq.py +334 -0
- plot_io/helpers/raincloud.py +249 -0
- plot_io/helpers/tree.py +214 -0
- plot_io/helpers/volcano.py +505 -0
- plot_io/hints.py +125 -0
- plot_io/kernels.py +740 -0
- plot_io/labels.py +566 -0
- plot_io/layers/__init__.py +100 -0
- plot_io/layers/base.py +630 -0
- plot_io/layers/context.py +87 -0
- plot_io/layers/core.py +446 -0
- plot_io/layers/geoms.py +1362 -0
- plot_io/layers/grammar.py +586 -0
- plot_io/layers/paint.py +614 -0
- plot_io/layers/pipeline.py +170 -0
- plot_io/layers/positions.py +431 -0
- plot_io/layers/stats.py +1088 -0
- plot_io/layout.py +1381 -0
- plot_io/legend.py +605 -0
- plot_io/levels.py +509 -0
- plot_io/limits.py +124 -0
- plot_io/lines.py +42 -0
- plot_io/mapped.py +522 -0
- plot_io/markers.py +110 -0
- plot_io/markup.py +128 -0
- plot_io/numbers.py +354 -0
- plot_io/occupancy.py +295 -0
- plot_io/plot.py +597 -0
- plot_io/presets/__init__.py +51 -0
- plot_io/presets/_util.py +153 -0
- plot_io/presets/area.py +145 -0
- plot_io/presets/bar.py +261 -0
- plot_io/presets/box.py +400 -0
- plot_io/presets/catpoints.py +177 -0
- plot_io/presets/contour.py +353 -0
- plot_io/presets/curves.py +30 -0
- plot_io/presets/dots.py +355 -0
- plot_io/presets/ecdf.py +97 -0
- plot_io/presets/errorbar.py +106 -0
- plot_io/presets/errors.py +296 -0
- plot_io/presets/fill.py +74 -0
- plot_io/presets/heatmap.py +322 -0
- plot_io/presets/hexbin.py +198 -0
- plot_io/presets/hist.py +391 -0
- plot_io/presets/hist2d.py +87 -0
- plot_io/presets/kde.py +162 -0
- plot_io/presets/kde2d.py +147 -0
- plot_io/presets/line.py +143 -0
- plot_io/presets/pie.py +502 -0
- plot_io/presets/regression.py +115 -0
- plot_io/presets/scatter.py +194 -0
- plot_io/presets/stem.py +100 -0
- plot_io/presets/violin.py +323 -0
- plot_io/py.typed +0 -0
- plot_io/registry.py +82 -0
- plot_io/render.py +480 -0
- plot_io/rows.py +491 -0
- plot_io/scales.py +103 -0
- plot_io/seams.py +138 -0
- plot_io/settings.py +807 -0
- plot_io/shapes.py +66 -0
- plot_io/sharing.py +232 -0
- plot_io/sizemaps.py +97 -0
- plot_io/spec.py +240 -0
- plot_io/states.py +216 -0
- plot_io/styles/__init__.py +307 -0
- plot_io/styles/library.py +397 -0
- plot_io/tables.py +138 -0
- plot_io/text.py +412 -0
- plot_io/ticks.py +400 -0
- plot_io/times.py +287 -0
- plot_io/titles.py +225 -0
- plot_io/transform.py +114 -0
- plot_io/types.py +13604 -0
- plot_io/units.py +768 -0
- plot_io/validators.py +1029 -0
- plot_io/values.py +190 -0
- plot_io-0.12.0.dist-info/METADATA +215 -0
- plot_io-0.12.0.dist-info/RECORD +130 -0
- plot_io-0.12.0.dist-info/WHEEL +4 -0
- plot_io-0.12.0.dist-info/licenses/LICENSE +28 -0
plot_io/defaults.py
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"""Every default setting of plot_io, in one place: the default look.
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``DEFAULTS`` maps setting names to their default values:
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* bare names are inherited settings (fonts, colors, line width, number formats, color maps,
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…): a figure passes them to its plots, a plot to its series, unless set lower down;
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* ``"Class.name"`` is the default of one setting of one class. A class without an entry
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of its own uses its base class's (``Fill.opacity`` overrides ``Series.opacity``).
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* ``"XAxis.name"``/``"YAxis.name"`` is the default of one axis, before ``"Axis.name"``.
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Values are plain data, parsed by each setting's validator: units (``"1.2em"``, ``"60%"``),
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``var()`` and ``calc()`` express defaults that depend on other settings (a title's size
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follows the plot's font size). ``DEFAULTS`` is the ``"default"`` style, the last of
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every figure's style chain; it is read-only (styles change the look). ``None``
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means unset (no value, inherit, or off); ``"auto"`` means chosen when drawing by a rule
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the setting's doc states, or that the setting's other defaults parametrize
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(``Axis.padding`` and ``Axis.auto_padding``, ``Axis.max_ticks`` and ``Axis.tick_spacing``).
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"""
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from collections.abc import Iterator, Mapping
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from typing import Any, NoReturn
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__all__ = ["DEFAULTS", "inherited", "default_of"]
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_DEFAULTS: dict[str, Any] = {
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# Inherited settings
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"font_size": 11.0,
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"font_family": ("Helvetica, Nimbus Sans, Nimbus Sans L, TeX Gyre Heros, FreeSans, Arial, "
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"Liberation Sans, Arimo"),
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"font_stretch": "normal",
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"font_variations": None,
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"font_optical_sizing": "auto",
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"line_height": 1.0,
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"markup": True,
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"text_color": "black",
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"line_width": 0.5,
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"opacity": 1.0,
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"rasterize": False,
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"simplify": "auto",
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"qualitative_map": "tab10_custom",
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"sequential_map": "rainbow_lc",
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"diverging_map": "blue_white_red_hc",
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"cyclic_map": "romao",
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"decimal_separator": ".",
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"thousands_separator": "",
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"minus": "hyphen",
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"prefix": "",
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"suffix": "",
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"precision": None,
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"color_variant": "forest",
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"plain_color": None,
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"data": None,
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# Setting groups: defaults of every embedding of a member (an owner's key comes first)
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"Marker.marker": "circle",
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"Marker.size": 4.5,
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"Marker.color": None,
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"Dendrogram.color": None,
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"Dendrogram.clusters": None,
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"Dendrogram.orientation": "vertical",
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"QQ.dist": "normal",
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"QQ.pvalues": False,
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"QQ.line": "auto",
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"QQ.band": "auto",
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"QQ.band_opacity": 0.2,
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"QQ.edge_color": None,
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"Raincloud.color": None,
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"Raincloud.parts": ("violin", "box", "points"),
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"Raincloud.orientation": "vertical",
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"Raincloud.width": "100%",
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"Raincloud.violin_width": "45%",
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"Raincloud.box_width": "8%",
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"Raincloud.points_offset": "-22%",
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"Raincloud.jitter": "8%",
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"Raincloud.seed": 0,
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"Raincloud.fill_opacity": 0.4,
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"Raincloud.bandwidth": "scott",
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"Raincloud.adjust": 1.0,
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"Raincloud.cut": 2.0,
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"Raincloud.points": 512,
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"Raincloud.whiskers": 1.5,
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"Raincloud.weights": None,
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"Raincloud.median_width": "calc(2 * var(line_width))",
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"Raincloud.marker_size": 3.0,
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"Raincloud.marker_edge_color": None,
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"Raincloud.categories": None,
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"Volcano.fold_change_threshold": 1.0,
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"Volcano.p_threshold": 0.05,
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"Volcano.colors": {"up": "#d6604d", "down": "#4393c3", "n.s.": "#bdbdbd"},
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"Volcano.counts": True,
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"Volcano.thresholds": True,
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"Volcano.threshold_color": "#808080",
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"Volcano.threshold_width": "var(line_width)",
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"Volcano.label": "top",
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"Volcano.label_count": 10,
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"Ma.fold_change_threshold": 1.0,
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"Ma.p_threshold": 0.05,
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"Ma.colors": {"up": "#d6604d", "down": "#4393c3", "n.s.": "#bdbdbd"},
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"Ma.counts": True,
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"Ma.thresholds": True,
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"Ma.threshold_color": "#808080",
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"Ma.threshold_width": "var(line_width)",
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"Ma.label": "top",
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"Ma.label_count": 10,
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"Manhattan.chr_sizes": None,
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"Manhattan.colors": ("#2c5d8f", "#8fb0d3"),
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"Manhattan.threshold": 5e-8,
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"Manhattan.threshold_color": "#808080",
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"Manhattan.threshold_width": "var(line_width)",
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"Manhattan.label": "top",
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"Manhattan.label_count": 10,
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"Marker.edge_color": "auto",
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"Marker.edge_width": 0.5,
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"Marker.fill": True,
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"Marker.fill_opacity": 1.0,
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"Marker.size_basis": "area",
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"Stroke.line_width": 0.5,
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"Stroke.line_style": "solid",
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"Stroke.cap": "butt",
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"Stroke.join": "round",
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"TextStyle.font_size": "1em",
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"TextStyle.font_weight": "normal",
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"TextStyle.font_style": "normal",
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"TextStyle.color": "var(text_color)",
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# Figures: size, arrangement, spacing, output
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"Figure.layout": "auto",
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"Figure.rows": None,
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"Figure.cols": None,
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"Figure.fill_order": "auto",
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"Figure.align": "axes",
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"Figure.widths": None,
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"Figure.heights": None,
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"Figure.width": "150px",
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"Figure.height": "calc(var(width) / var(aspect_ratio))",
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"Figure.aspect_ratio": 5 / 4,
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"Figure.reference": "axes",
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"Figure.spacing": 13.0,
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"Figure.margin": 5.0,
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"Figure.background": "white",
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"Figure.default_dpi": "4x",
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"Figure.quality": "auto",
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"Figure.fonts": None,
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"Figure.share_x": None,
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"Figure.share_color": False,
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"Figure.share_size": False,
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"Figure.share_legend": False,
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"Figure.share_y": None,
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"Figure.share": None,
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"Figure.label_outer": None,
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"Figure.style": None,
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"Figure.scaling": 1.0,
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"Figure.vars": None,
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# Titles (plot and figure titles)
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"TitleBase.text": None,
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"TitleBase.side": "top",
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"TitleBase.align": "center",
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"TitleBase.over": "axes",
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"TitleBase.rotation": "auto",
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"TitleBase.pad": 5.0,
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"TitleBase.order": None,
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"TitleBase.rule": False,
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"TitleBase.rule_color": "var(color)",
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"TitleBase.rule_width": "var(line_width)",
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"TitleBase.rule_gap": "0.5em",
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# Figure titles
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"FigureTitle.font_weight": "bold",
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"FigureTitle.pad": "0.5em",
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# Plots
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"Plot.spines": "bottom left",
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"Plot.data_ratio": None,
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"Plot.background": None,
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"Plot.border_color": None,
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"Plot.clip": True,
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"Plot.axes": True,
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"Plot.share_x": None,
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"Plot.share_y": None,
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"Plot.share": None,
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"Plot.vars": None,
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"Plot.space_above": 0.0,
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# Figure legends (the other settings: Legend.*)
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"FigureLegend.side": "right",
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"FigureLegend.align": "center",
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"FigureLegend.order": None,
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# Legends
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"Legend.inside": "auto",
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"Legend.side": None,
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"Legend.align": "auto",
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"Legend.visible": True,
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"Legend.columns": 1,
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"Legend.frame": False,
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"Legend.title": "auto",
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"Legend.background": "white",
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"Legend.frame_color": "#999999",
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"Legend.pad": 5.0,
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"Legend.frame_radius": 0.0,
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"Legend.frame_opacity": 1.0,
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"Legend.glyph_opacity": None,
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"Legend.glyph": "series",
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"Legend.orientation": "auto",
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"Legend.glyph_length": "1.4em",
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"Legend.row_height": "1.35em",
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"Legend.glyph_gap": "0.5em",
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"Legend.column_gap": "1em",
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"Legend.inner_pad": "auto",
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"Legend.title_gap": "0.3em",
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# Size legends (a size key in its own grid area)
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"SizeLegend.values": None,
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"SizeLegend.title": None,
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"SizeLegend.font_size": None,
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# Axes
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"Axis.label": None,
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221
|
+
"Axis.label_position": "axis",
|
|
222
|
+
"Axis.region": None,
|
|
223
|
+
"Axis.chr_sizes": None,
|
|
224
|
+
"Axis.scale_bar": False,
|
|
225
|
+
"Axis.unit": "auto",
|
|
226
|
+
"Axis.unit_in": "label",
|
|
227
|
+
"Axis.origin": None,
|
|
228
|
+
"Axis.region_widths": "span",
|
|
229
|
+
"Axis.region_gap": "1em",
|
|
230
|
+
"Axis.scale": None,
|
|
231
|
+
"Axis.linthresh": 1.0,
|
|
232
|
+
"Axis.tz": None,
|
|
233
|
+
"Axis.limits": "auto",
|
|
234
|
+
"ColorAxis.center": None,
|
|
235
|
+
"ColorAxis.color_map": "auto",
|
|
236
|
+
"Axis.padding": "auto",
|
|
237
|
+
"Axis.auto_padding": "5%",
|
|
238
|
+
"Axis.sticky": True,
|
|
239
|
+
"Axis.invert": False,
|
|
240
|
+
"Axis.ticks": None,
|
|
241
|
+
"Axis.tick_labels": None,
|
|
242
|
+
"Axis.minor_ticks": None,
|
|
243
|
+
"Axis.tick_format": "auto",
|
|
244
|
+
"Axis.tick_rotation": "auto",
|
|
245
|
+
"Axis.max_ticks": "auto",
|
|
246
|
+
"Axis.tick_spacing": ("3em", "2em"),
|
|
247
|
+
"Axis.time_tick_spacing": ("5em", "2.5em"),
|
|
248
|
+
"Axis.tick_label_gap": "0.6em",
|
|
249
|
+
"Axis.category_label_spacing": ("1.6em", "1.3em"),
|
|
250
|
+
"Axis.label_min_size": "6pt",
|
|
251
|
+
"Axis.auto_max_ticks": (10, 8),
|
|
252
|
+
"Axis.sci_limits": (-4, 5),
|
|
253
|
+
"Axis.tick_length": 6.0,
|
|
254
|
+
"Axis.minor_tick_length": "60%",
|
|
255
|
+
"Axis.tick_direction": "out",
|
|
256
|
+
"Axis.tick_pad": 5.0,
|
|
257
|
+
"Axis.label_pad": 5.0,
|
|
258
|
+
"Axis.color": "var(text_color)",
|
|
259
|
+
"Axis.line_color": "var(color)",
|
|
260
|
+
"Axis.tick_color": "var(color)",
|
|
261
|
+
"Axis.tick_label_color": "var(color)",
|
|
262
|
+
"Axis.label_color": "var(color)",
|
|
263
|
+
"XAxis.side": "bottom",
|
|
264
|
+
"YAxis.side": "left",
|
|
265
|
+
"Axis.side": "left",
|
|
266
|
+
"Axis.mirror": False,
|
|
267
|
+
"Axis.spine_offset": 0.0,
|
|
268
|
+
"Axis.spine_trim": False,
|
|
269
|
+
"Axis.include_zero": False,
|
|
270
|
+
"Axis.zero_line": False,
|
|
271
|
+
"Axis.zero_line_color": "var(line_color)",
|
|
272
|
+
"Axis.zero_line_width": "var(line_width)",
|
|
273
|
+
"Axis.snap": ("4%", "8%"),
|
|
274
|
+
"Axis.grid": False,
|
|
275
|
+
"Axis.grid_color": "#dddddd",
|
|
276
|
+
"Axis.minor_grid": False,
|
|
277
|
+
"Axis.minor_grid_color": "var(grid_color)",
|
|
278
|
+
"Axis.minor_grid_width": "50%",
|
|
279
|
+
"Axis.minor_grid_style": "var(grid_style)",
|
|
280
|
+
"Axis.visible": True,
|
|
281
|
+
|
|
282
|
+
# Size axes (color axes take the Axis defaults, and colorbar keys)
|
|
283
|
+
"SizeAxis.size_map": None,
|
|
284
|
+
|
|
285
|
+
# Colorbars
|
|
286
|
+
"Colorbar.side": "bottom",
|
|
287
|
+
"Colorbar.inside": None,
|
|
288
|
+
"Colorbar.align": "center",
|
|
289
|
+
"Colorbar.order": None,
|
|
290
|
+
"Colorbar.style": "key",
|
|
291
|
+
"Colorbar.orientation": "auto",
|
|
292
|
+
"Colorbar.thickness": "auto",
|
|
293
|
+
"Colorbar.length": "auto",
|
|
294
|
+
"Colorbar.values": "limits",
|
|
295
|
+
"Colorbar.value_gap": "0.6em",
|
|
296
|
+
"Colorbar.label_gap": "1.2em",
|
|
297
|
+
"Colorbar.label_position": "end",
|
|
298
|
+
"Colorbar.pad": "auto",
|
|
299
|
+
"Colorbar.label": None,
|
|
300
|
+
"Colorbar.extend": "auto",
|
|
301
|
+
"Colorbar.extend_shape": "auto",
|
|
302
|
+
"Colorbar.frame": False,
|
|
303
|
+
"Colorbar.count": 3,
|
|
304
|
+
"Colorbar.marker_gap": "0.4em",
|
|
305
|
+
"Colorbar.frame_color": "#666666",
|
|
306
|
+
"Decoration.name": None,
|
|
307
|
+
"Decoration.opacity": 1.0,
|
|
308
|
+
"Decoration.z": 1.0,
|
|
309
|
+
"Decoration.extend_limits": False,
|
|
310
|
+
"Decoration.clip": True,
|
|
311
|
+
"HLine.color": "#4d4d4d",
|
|
312
|
+
"HLine.min": "0%",
|
|
313
|
+
"HLine.max": "100%",
|
|
314
|
+
"VLine.color": "#4d4d4d",
|
|
315
|
+
"VLine.min": "0%",
|
|
316
|
+
"VLine.max": "100%",
|
|
317
|
+
"AxLine.color": "#4d4d4d",
|
|
318
|
+
"HSpan.color": "#e5e5e5",
|
|
319
|
+
"HSpan.edge_color": None,
|
|
320
|
+
"HSpan.edge_width": 0.0,
|
|
321
|
+
"HSpan.min": "0%",
|
|
322
|
+
"HSpan.max": "100%",
|
|
323
|
+
"HSpan.z": -1.0,
|
|
324
|
+
"VSpan.color": "#e5e5e5",
|
|
325
|
+
"VSpan.edge_color": None,
|
|
326
|
+
"VSpan.edge_width": 0.0,
|
|
327
|
+
"VSpan.min": "0%",
|
|
328
|
+
"VSpan.max": "100%",
|
|
329
|
+
"VSpan.z": -1.0,
|
|
330
|
+
"Text.align": "left",
|
|
331
|
+
"Text.valign": "baseline",
|
|
332
|
+
"Text.rotation": 0.0,
|
|
333
|
+
"Text.coords": "data",
|
|
334
|
+
"Text.clip": False,
|
|
335
|
+
"Annotate.align": "center",
|
|
336
|
+
"Annotate.valign": "center",
|
|
337
|
+
"Annotate.text_coords": "var(coords)",
|
|
338
|
+
"Annotate.arrow": True,
|
|
339
|
+
"Annotate.arrow_style": "->",
|
|
340
|
+
"Annotate.arrow_color": "var(color)",
|
|
341
|
+
"Annotate.head_length": 7.0,
|
|
342
|
+
"Annotate.shrink": 3.0,
|
|
343
|
+
"Bracket.color": "var(text_color)",
|
|
344
|
+
"Bracket.y": None,
|
|
345
|
+
"Bracket.format": "stars",
|
|
346
|
+
"Bracket.stars": (0.05, 0.01, 0.001, 0.0001),
|
|
347
|
+
"Bracket.tip": "0.4em",
|
|
348
|
+
"Bracket.step": "8%",
|
|
349
|
+
"Bracket.gap": "0.15em",
|
|
350
|
+
"Bracket.extend_limits": True,
|
|
351
|
+
"Bracket.clip": False,
|
|
352
|
+
|
|
353
|
+
# Every series
|
|
354
|
+
"Series.name": None,
|
|
355
|
+
"Series.markers": None,
|
|
356
|
+
"Series.line_styles": None,
|
|
357
|
+
"Series.level_order": None,
|
|
358
|
+
"Series.level_missing": "keep",
|
|
359
|
+
"Series.estimate": None,
|
|
360
|
+
"Series.interval": None,
|
|
361
|
+
"Series.color_limits": None,
|
|
362
|
+
"Series.color_scale": None,
|
|
363
|
+
"Series.center": None,
|
|
364
|
+
"Series.color_map": "auto",
|
|
365
|
+
"Series.color_axis": None,
|
|
366
|
+
"Series.colorbar": False,
|
|
367
|
+
"Series.size_limits": None,
|
|
368
|
+
"Series.size_scale": None,
|
|
369
|
+
"Series.size_axis": None,
|
|
370
|
+
"Series.z": None,
|
|
371
|
+
"Series.x_origin": None,
|
|
372
|
+
"Series.x_scale": 1.0,
|
|
373
|
+
"Series.x_extent": None,
|
|
374
|
+
"Series.y_origin": None,
|
|
375
|
+
"Series.y_scale": 1.0,
|
|
376
|
+
"Series.y_extent": None,
|
|
377
|
+
|
|
378
|
+
# Scatter
|
|
379
|
+
"Scatter.size_map": None,
|
|
380
|
+
"Scatter.size_key": "key",
|
|
381
|
+
"Scatter.draw_order": None,
|
|
382
|
+
"Scatter.opacity_range": (0.2, 1.0),
|
|
383
|
+
"Scatter.x_error": None,
|
|
384
|
+
"Scatter.y_error": None,
|
|
385
|
+
"Scatter.orientation": "vertical",
|
|
386
|
+
"Scatter.labels": None,
|
|
387
|
+
"Scatter.label_font_size": "0.9em",
|
|
388
|
+
"Scatter.label_color": None,
|
|
389
|
+
"Scatter.label_reach": "6em",
|
|
390
|
+
"Scatter.label_leaders": True,
|
|
391
|
+
|
|
392
|
+
# Line
|
|
393
|
+
"Line.color": None,
|
|
394
|
+
"Line.interpolation": "linear",
|
|
395
|
+
"Line.missing": "break",
|
|
396
|
+
"Line.orientation": "vertical",
|
|
397
|
+
"Line.x_error": None,
|
|
398
|
+
"Line.y_error": None,
|
|
399
|
+
"Line.show_markers": False,
|
|
400
|
+
"Line.interval_style": "band",
|
|
401
|
+
|
|
402
|
+
# Fill
|
|
403
|
+
"Fill.color": None,
|
|
404
|
+
"Fill.color_below": None,
|
|
405
|
+
"Fill.opacity": "calc(0.3 * inherit)",
|
|
406
|
+
"Fill.edge_color": None,
|
|
407
|
+
"Fill.edge_width": "var(line_width)",
|
|
408
|
+
"Fill.interpolation": "linear",
|
|
409
|
+
"Fill.missing": "break",
|
|
410
|
+
"Fill.orientation": "vertical",
|
|
411
|
+
|
|
412
|
+
# Area
|
|
413
|
+
"Area.orientation": "vertical",
|
|
414
|
+
"Area.baseline": "zero",
|
|
415
|
+
"Area.stack": True,
|
|
416
|
+
"Area.color": None,
|
|
417
|
+
"Area.fill": True,
|
|
418
|
+
"Area.fill_opacity": 0.25,
|
|
419
|
+
"Area.edge_color": "series",
|
|
420
|
+
"Area.edge_width": "var(line_width)",
|
|
421
|
+
"Area.interpolation": "linear",
|
|
422
|
+
"Area.missing": "break",
|
|
423
|
+
|
|
424
|
+
# Error bars
|
|
425
|
+
"Errorbar.orientation": "vertical",
|
|
426
|
+
"Errorbar.marker": None,
|
|
427
|
+
"Errorbar.color": None,
|
|
428
|
+
"Errorbar.cap_length": 4.0,
|
|
429
|
+
"Errorbar.x_error": None,
|
|
430
|
+
"Errorbar.y_error": None,
|
|
431
|
+
"Errorbar.y_error_style": "bars",
|
|
432
|
+
"Errorbar.band_opacity": 0.25,
|
|
433
|
+
|
|
434
|
+
# Stem
|
|
435
|
+
"Stem.marker_size": 5.0,
|
|
436
|
+
"Stem.marker_edge_color": None,
|
|
437
|
+
"Stem.marker_edge_width": 0.0,
|
|
438
|
+
"Stem.color": None,
|
|
439
|
+
"Stem.baseline": 0.0,
|
|
440
|
+
"Stem.baseline_color": "#4d4d4d",
|
|
441
|
+
"Stem.orientation": "vertical",
|
|
442
|
+
|
|
443
|
+
# Regression
|
|
444
|
+
"Regression.orientation": "vertical",
|
|
445
|
+
"Regression.order": 1,
|
|
446
|
+
"Regression.lowess": False,
|
|
447
|
+
"Regression.frac": 0.6666666666666666,
|
|
448
|
+
"Regression.weights": None,
|
|
449
|
+
"Regression.ci": 95.0,
|
|
450
|
+
"Regression.logx": False,
|
|
451
|
+
"Regression.scatter": True,
|
|
452
|
+
"Regression.range": None,
|
|
453
|
+
"Regression.points": 100,
|
|
454
|
+
"Regression.color": None,
|
|
455
|
+
"Regression.band_opacity": 0.2,
|
|
456
|
+
|
|
457
|
+
# Bar
|
|
458
|
+
"Bar.color": None,
|
|
459
|
+
"Bar.edge_color": "series",
|
|
460
|
+
"Bar.edge_width": "var(line_width)",
|
|
461
|
+
"Bar.fill": True,
|
|
462
|
+
"Bar.fill_opacity": 0.25,
|
|
463
|
+
"Bar.seam_color": "white",
|
|
464
|
+
"Bar.width": "80%",
|
|
465
|
+
"Bar.max_width": None,
|
|
466
|
+
"Bar.bottom": 0.0,
|
|
467
|
+
"Bar.orientation": "vertical",
|
|
468
|
+
"Bar.stack": False,
|
|
469
|
+
"Bar.dodge": True,
|
|
470
|
+
"Bar.gap": "15%",
|
|
471
|
+
"Bar.saturation": 1.0,
|
|
472
|
+
"Bar.y_error": None,
|
|
473
|
+
"Bar.error_color": "#333333",
|
|
474
|
+
"Bar.value_labels": False,
|
|
475
|
+
"Bar.value_label_format": "auto",
|
|
476
|
+
|
|
477
|
+
# Histogram
|
|
478
|
+
"Hist.bins": "auto",
|
|
479
|
+
"Hist.range": None,
|
|
480
|
+
"Hist.weights": None,
|
|
481
|
+
"Hist.stat": "count",
|
|
482
|
+
"Hist.cumulative": False,
|
|
483
|
+
"Hist.shape": "stepfilled",
|
|
484
|
+
"Hist.bins_scale": "axis",
|
|
485
|
+
"Hist.orientation": "vertical",
|
|
486
|
+
"Hist.stack": False,
|
|
487
|
+
"Hist.dodge": False,
|
|
488
|
+
"Hist.color": None,
|
|
489
|
+
"Hist.edge_color": None,
|
|
490
|
+
"Hist.edge_width": 0.0,
|
|
491
|
+
"Hist.line_color": None,
|
|
492
|
+
"Hist.outline": True,
|
|
493
|
+
"Hist.fill": True,
|
|
494
|
+
"Hist.fill_opacity": "auto",
|
|
495
|
+
"Hist.saturation": 1.0,
|
|
496
|
+
"Hist.value_labels": False,
|
|
497
|
+
"Hist.value_label_format": "auto",
|
|
498
|
+
|
|
499
|
+
# Density curves
|
|
500
|
+
"Kde.bandwidth": "scott",
|
|
501
|
+
"Kde.adjust": 1.0,
|
|
502
|
+
"Kde.cut": 3.0,
|
|
503
|
+
"Kde.range": None,
|
|
504
|
+
"Kde.points": 512,
|
|
505
|
+
"Kde.cumulative": False,
|
|
506
|
+
"Kde.fill": False,
|
|
507
|
+
"Kde.fill_opacity": 0.25,
|
|
508
|
+
"Kde.weights": None,
|
|
509
|
+
"Kde.orientation": "vertical",
|
|
510
|
+
"Kde.stack": False,
|
|
511
|
+
"Kde.color": None,
|
|
512
|
+
|
|
513
|
+
# ECDF
|
|
514
|
+
"Ecdf.weights": None,
|
|
515
|
+
"Ecdf.stat": "proportion",
|
|
516
|
+
"Ecdf.complementary": False,
|
|
517
|
+
"Ecdf.stack": False,
|
|
518
|
+
"Ecdf.orientation": "vertical",
|
|
519
|
+
"Ecdf.color": None,
|
|
520
|
+
|
|
521
|
+
# Box plots
|
|
522
|
+
"Box.color": None,
|
|
523
|
+
"Box.edge_color": "series",
|
|
524
|
+
"Box.edge_width": "var(line_width)",
|
|
525
|
+
"Box.fill": True,
|
|
526
|
+
"Box.fill_opacity": 0.25,
|
|
527
|
+
"Box.whisker_color": None,
|
|
528
|
+
"Box.whisker_width": "var(edge_width)",
|
|
529
|
+
"Box.median_color": None,
|
|
530
|
+
"Box.median_width": "calc(3 * var(edge_width))",
|
|
531
|
+
"Box.width": "80%",
|
|
532
|
+
"Box.offset": 0.0,
|
|
533
|
+
"Box.max_width": "60%",
|
|
534
|
+
"Box.cap_length": "50%",
|
|
535
|
+
"Box.whiskers": 1.5,
|
|
536
|
+
"Box.weights": None,
|
|
537
|
+
"Box.outliers": True,
|
|
538
|
+
"Box.saturation": 1.0,
|
|
539
|
+
"Box.mean": False,
|
|
540
|
+
"Box.mean_marker": "diamond",
|
|
541
|
+
"Box.mean_color": "white",
|
|
542
|
+
"Box.orientation": "vertical",
|
|
543
|
+
"Box.dodge": True,
|
|
544
|
+
"Box.gap": "15%",
|
|
545
|
+
"Box.categories": None,
|
|
546
|
+
"Box.marker_size": 3.5,
|
|
547
|
+
"Box.marker_edge_color": None,
|
|
548
|
+
|
|
549
|
+
# Violins
|
|
550
|
+
"Violin.color": None,
|
|
551
|
+
"Violin.edge_color": "series",
|
|
552
|
+
"Violin.edge_width": "var(line_width)",
|
|
553
|
+
"Violin.saturation": 1.0,
|
|
554
|
+
"Violin.fill": True,
|
|
555
|
+
"Violin.fill_opacity": 0.25,
|
|
556
|
+
"Violin.width": "80%",
|
|
557
|
+
"Violin.max_width": None,
|
|
558
|
+
"Violin.bandwidth": "scott",
|
|
559
|
+
"Violin.weights": None,
|
|
560
|
+
"Violin.adjust": 1.0,
|
|
561
|
+
"Violin.cut": 2.0,
|
|
562
|
+
"Violin.points": 512,
|
|
563
|
+
"Violin.width_scale": "area",
|
|
564
|
+
"Violin.inner": "box",
|
|
565
|
+
"Violin.split": False,
|
|
566
|
+
"Violin.side": "both",
|
|
567
|
+
"Violin.orientation": "vertical",
|
|
568
|
+
"Violin.dodge": True,
|
|
569
|
+
"Violin.gap": "15%",
|
|
570
|
+
"Violin.categories": None,
|
|
571
|
+
"Strip.size_map": None,
|
|
572
|
+
"Strip.size_key": "key",
|
|
573
|
+
"Strip.orientation": "vertical",
|
|
574
|
+
"Strip.width": "80%",
|
|
575
|
+
"Strip.offset": 0.0,
|
|
576
|
+
"Strip.max_width": None,
|
|
577
|
+
"Strip.dodge": True,
|
|
578
|
+
"Strip.gap": "15%",
|
|
579
|
+
"Strip.categories": None,
|
|
580
|
+
"Strip.jitter": "10%",
|
|
581
|
+
"Strip.seed": 0,
|
|
582
|
+
"Strip.draw_order": None,
|
|
583
|
+
"Strip.opacity_range": (0.2, 1.0),
|
|
584
|
+
"Swarm.size_map": None,
|
|
585
|
+
"Swarm.size_key": "key",
|
|
586
|
+
"Swarm.orientation": "vertical",
|
|
587
|
+
"Swarm.width": "80%",
|
|
588
|
+
"Swarm.offset": 0.0,
|
|
589
|
+
"Swarm.max_width": None,
|
|
590
|
+
"Swarm.dodge": True,
|
|
591
|
+
"Swarm.gap": "15%",
|
|
592
|
+
"Swarm.categories": None,
|
|
593
|
+
"Swarm.draw_order": None,
|
|
594
|
+
"Swarm.opacity_range": (0.2, 1.0),
|
|
595
|
+
|
|
596
|
+
# Heatmaps
|
|
597
|
+
"Heatmap.kind": "image",
|
|
598
|
+
"Heatmap.nan_color": None,
|
|
599
|
+
"Heatmap.origin": "top",
|
|
600
|
+
"Heatmap.value_labels": False,
|
|
601
|
+
"Heatmap.value_label_format": "auto",
|
|
602
|
+
"Heatmap.value_label_font_size": "0.9em",
|
|
603
|
+
# Dot plots
|
|
604
|
+
"Dots.size_map": (0.0, 12.0),
|
|
605
|
+
"Dots.size_limits": "0/max",
|
|
606
|
+
"Dots.size_key": "key",
|
|
607
|
+
"Dots.scale_color": None,
|
|
608
|
+
"Dots.origin": "top",
|
|
609
|
+
"Dots.colorbar": True,
|
|
610
|
+
|
|
611
|
+
# 2-D histograms
|
|
612
|
+
"Hist2d.bins": ("auto", "auto"),
|
|
613
|
+
"Hist2d.range": None,
|
|
614
|
+
"Hist2d.weights": None,
|
|
615
|
+
"Hist2d.stat": "count",
|
|
616
|
+
"Hist2d.min_count": 1.0,
|
|
617
|
+
"Hist2d.origin": "bottom",
|
|
618
|
+
|
|
619
|
+
# Hexagonal bins
|
|
620
|
+
"Hexbin.bins": 30,
|
|
621
|
+
"Hexbin.weights": None,
|
|
622
|
+
"Hexbin.stat": "count",
|
|
623
|
+
"Hexbin.min_count": 1.0,
|
|
624
|
+
"Hexbin.edge_color": None,
|
|
625
|
+
"Hexbin.edge_width": 0.0,
|
|
626
|
+
|
|
627
|
+
# Contours
|
|
628
|
+
"Contour.levels": 10,
|
|
629
|
+
"Contour.fill": False,
|
|
630
|
+
"Contour.fill_opacity": 1.0,
|
|
631
|
+
"Contour.lines": True,
|
|
632
|
+
"Contour.negative_style": None,
|
|
633
|
+
"Contour.opacity": 1.0,
|
|
634
|
+
"Contour.value_labels": False,
|
|
635
|
+
"Contour.value_label_format": "auto",
|
|
636
|
+
"Contour.value_label_font_size": "0.8em",
|
|
637
|
+
|
|
638
|
+
# 2-D densities (contours of a density)
|
|
639
|
+
"Kde2d.thresh": 0.05,
|
|
640
|
+
"Kde2d.bandwidth": "scott",
|
|
641
|
+
"Kde2d.adjust": 1.0,
|
|
642
|
+
"Kde2d.weights": None,
|
|
643
|
+
"Kde2d.cut": 3.0,
|
|
644
|
+
"Kde2d.points": 128,
|
|
645
|
+
|
|
646
|
+
# Pies
|
|
647
|
+
"Pie.names": None,
|
|
648
|
+
"Pie.start": 90.0,
|
|
649
|
+
"Pie.counterclockwise": True,
|
|
650
|
+
"Pie.hole": 0.0,
|
|
651
|
+
"Pie.explode": None,
|
|
652
|
+
"Pie.sort": False,
|
|
653
|
+
"Pie.name_position": "outside",
|
|
654
|
+
"Pie.value_labels": False,
|
|
655
|
+
"Pie.value_label_format": "auto",
|
|
656
|
+
"Pie.label_spacing": "1.25em",
|
|
657
|
+
"Pie.edge_color": "series",
|
|
658
|
+
"Pie.edge_width": 1.25,
|
|
659
|
+
"Pie.opacity": 1.0,
|
|
660
|
+
"Pie.fill": True,
|
|
661
|
+
"Pie.fill_opacity": 0.25,
|
|
662
|
+
"Pie.seam_color": "white",
|
|
663
|
+
# Lines and bands through rows, groups of rows (figure.vline, vspan, group)
|
|
664
|
+
"FigureVLine.color": "#4d4d4d",
|
|
665
|
+
"FigureVLine.line_style": "dashed",
|
|
666
|
+
"FigureVLine.opacity": 1.0,
|
|
667
|
+
"FigureVSpan.color": "#e5e5e5",
|
|
668
|
+
"FigureVSpan.opacity": 1.0,
|
|
669
|
+
"FigureGroup.label": None,
|
|
670
|
+
"FigureGroup.letter": None,
|
|
671
|
+
"FigureGroup.font_size": "1em",
|
|
672
|
+
"FigureGroup.letter_font_size": "1.4em",
|
|
673
|
+
"FigureGroup.letter_weight": "bold",
|
|
674
|
+
"FigureGroup.pad": "0.5em",
|
|
675
|
+
# Genome tracks
|
|
676
|
+
"Track.height": "auto",
|
|
677
|
+
"Track.auto_height": "4.5em",
|
|
678
|
+
"Track.space_above": "auto",
|
|
679
|
+
"Track.auto_space_above": "0.6em",
|
|
680
|
+
"Track.lane_gap": "0.3em",
|
|
681
|
+
"Track.fill_mode": None,
|
|
682
|
+
"GenomeSeries.region": None,
|
|
683
|
+
"BigWig.bins": "0.5px",
|
|
684
|
+
"BigWig.bin_mode": "mean",
|
|
685
|
+
"BigWig.def_value": 0.0,
|
|
686
|
+
"BigWig.kind": "step",
|
|
687
|
+
"BigWig.fill_to": 0.0,
|
|
688
|
+
"BigWig.fill": True,
|
|
689
|
+
"BigWig.fill_opacity": 0.2,
|
|
690
|
+
"BigWig.color": None,
|
|
691
|
+
"BigWig.transform": None,
|
|
692
|
+
"BigWig.lane": "below",
|
|
693
|
+
"BigWig.row_height": "1.2em",
|
|
694
|
+
"Bed.lane": "below",
|
|
695
|
+
"Bed.kind": "boxes",
|
|
696
|
+
"Bed.rows": "collapse",
|
|
697
|
+
"Bed.max_rows": 20,
|
|
698
|
+
"Bed.min_width": 0.75,
|
|
699
|
+
"Bed.color": "black",
|
|
700
|
+
"Bed.names": False,
|
|
701
|
+
"Bed.name_position": "auto",
|
|
702
|
+
"Bed.name_region": None,
|
|
703
|
+
"Bed.recolor": False,
|
|
704
|
+
"Bed.nan_color": "gray",
|
|
705
|
+
"Bed.outline": True,
|
|
706
|
+
"Bed.fill": True,
|
|
707
|
+
"Bed.fill_opacity": 0.3,
|
|
708
|
+
"Bed.strand": False,
|
|
709
|
+
"Bed.row_height": "1.2em",
|
|
710
|
+
"Bed.name_font_size": "0.85em",
|
|
711
|
+
"Genes.kind": "genes",
|
|
712
|
+
"Genes.rows": "expand",
|
|
713
|
+
"Genes.names": True,
|
|
714
|
+
"Genes.strand": True,
|
|
715
|
+
"Genes.outline": False,
|
|
716
|
+
"Genes.fill_opacity": 1.0,
|
|
717
|
+
"Gtf.model": "gene",
|
|
718
|
+
"Gtf.gene_type": None,
|
|
719
|
+
"Gtf.transcript_type": None,
|
|
720
|
+
"HiC.depth": None,
|
|
721
|
+
"HiC.bins": "0.5px",
|
|
722
|
+
"HiC.normalization": "none",
|
|
723
|
+
"HiC.matrix_type": "observed",
|
|
724
|
+
"HiC.color_limits": "q:0.01/q:0.99",
|
|
725
|
+
"HiC.color_scale": "log",
|
|
726
|
+
"HiC.nan_color": None,
|
|
727
|
+
"HiC.direction": "up",
|
|
728
|
+
"HiC.max_height": None,
|
|
729
|
+
"HiC.fit": "clip",
|
|
730
|
+
"HiC.shape": "triangle",
|
|
731
|
+
"HiC.region2": None,
|
|
732
|
+
"Links.lane": "below",
|
|
733
|
+
"Links.direction": "up",
|
|
734
|
+
"Links.color": "black",
|
|
735
|
+
"Links.max_height": "4.5em",
|
|
736
|
+
"Links.outside": "clip",
|
|
737
|
+
"Links.nan_color": "gray",
|
|
738
|
+
# Site matrices (site_heatmap, site_profile)
|
|
739
|
+
"SiteHeatmap.flank": "5kb",
|
|
740
|
+
"SiteHeatmap.bins": 100,
|
|
741
|
+
"SiteHeatmap.anchor": "center",
|
|
742
|
+
"SiteHeatmap.bin_mode": "mean",
|
|
743
|
+
"SiteHeatmap.sort": "mean",
|
|
744
|
+
"SiteHeatmap.row_bins": "auto",
|
|
745
|
+
"SiteHeatmap.nan_color": None,
|
|
746
|
+
"SiteProfile.flank": "5kb",
|
|
747
|
+
"SiteProfile.bins": 100,
|
|
748
|
+
"SiteProfile.anchor": "center",
|
|
749
|
+
"SiteProfile.bin_mode": "mean",
|
|
750
|
+
"SiteProfile.stat": "mean",
|
|
751
|
+
"SiteProfile.band": None,
|
|
752
|
+
"SiteProfile.color": None,
|
|
753
|
+
"SiteProfile.fill_opacity": 0.2,
|
|
754
|
+
}
|
|
755
|
+
|
|
756
|
+
|
|
757
|
+
class _ReadOnly(Mapping[str, Any]):
|
|
758
|
+
"""``DEFAULTS``: a read-only view of the default values."""
|
|
759
|
+
|
|
760
|
+
__slots__ = ("_d",)
|
|
761
|
+
|
|
762
|
+
def __init__(self, d: dict[str, Any]) -> None:
|
|
763
|
+
self._d = d
|
|
764
|
+
|
|
765
|
+
def __getitem__(self, key: str) -> Any:
|
|
766
|
+
return self._d[key]
|
|
767
|
+
|
|
768
|
+
def __contains__(self, key: object) -> bool:
|
|
769
|
+
return key in self._d
|
|
770
|
+
|
|
771
|
+
def get(self, key: str, default: Any = None) -> Any:
|
|
772
|
+
return self._d.get(key, default)
|
|
773
|
+
|
|
774
|
+
def __iter__(self) -> Iterator[str]:
|
|
775
|
+
return iter(self._d)
|
|
776
|
+
|
|
777
|
+
def __len__(self) -> int:
|
|
778
|
+
return len(self._d)
|
|
779
|
+
|
|
780
|
+
def __repr__(self) -> str:
|
|
781
|
+
return f"DEFAULTS({self._d!r})"
|
|
782
|
+
|
|
783
|
+
def _refuse(self, *args: Any, **kwargs: Any) -> NoReturn:
|
|
784
|
+
raise TypeError("DEFAULTS is read-only: change settings with a style "
|
|
785
|
+
"(plt.set_style({...}), plt.use_style or plt.registry.styles.add)")
|
|
786
|
+
|
|
787
|
+
__setitem__ = __delitem__ = __ior__ = _refuse
|
|
788
|
+
update = pop = popitem = setdefault = clear = _refuse
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
DEFAULTS: Mapping[str, Any] = _ReadOnly(_DEFAULTS)
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
def inherited() -> dict[str, Any]:
|
|
795
|
+
"""The inherited settings of ``DEFAULTS`` (bare names), under every style's."""
|
|
796
|
+
return {k: v for k, v in DEFAULTS.items() if "." not in k}
|
|
797
|
+
|
|
798
|
+
|
|
799
|
+
def default_of(setting: Any, key: str) -> Any:
|
|
800
|
+
"""``DEFAULTS[key]`` (a key not in ``DEFAULTS``: the setting's declared default), text
|
|
801
|
+
and sequences parsed by ``setting``'s validator. ``ValueError`` when it rejects it."""
|
|
802
|
+
d = DEFAULTS[key] if key in DEFAULTS else setting.default
|
|
803
|
+
if isinstance(d, (str, tuple, list)):
|
|
804
|
+
from .settings import check_value
|
|
805
|
+
try:
|
|
806
|
+
d = check_value(setting, d)
|
|
807
|
+
except ValueError as e:
|
|
808
|
+
raise ValueError(f"default {key}: {e}") from None
|
|
809
|
+
return d
|