arviz 0.23.3__py3-none-any.whl → 1.0.0rc0__py3-none-any.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.
- arviz/__init__.py +52 -367
- arviz-1.0.0rc0.dist-info/METADATA +182 -0
- arviz-1.0.0rc0.dist-info/RECORD +5 -0
- {arviz-0.23.3.dist-info → arviz-1.0.0rc0.dist-info}/WHEEL +1 -2
- {arviz-0.23.3.dist-info → arviz-1.0.0rc0.dist-info}/licenses/LICENSE +0 -1
- arviz/data/__init__.py +0 -55
- arviz/data/base.py +0 -596
- arviz/data/converters.py +0 -203
- arviz/data/datasets.py +0 -161
- arviz/data/example_data/code/radon/radon.json +0 -326
- arviz/data/example_data/data/centered_eight.nc +0 -0
- arviz/data/example_data/data/non_centered_eight.nc +0 -0
- arviz/data/example_data/data_local.json +0 -12
- arviz/data/example_data/data_remote.json +0 -58
- arviz/data/inference_data.py +0 -2386
- arviz/data/io_beanmachine.py +0 -112
- arviz/data/io_cmdstan.py +0 -1036
- arviz/data/io_cmdstanpy.py +0 -1233
- arviz/data/io_datatree.py +0 -23
- arviz/data/io_dict.py +0 -462
- arviz/data/io_emcee.py +0 -317
- arviz/data/io_json.py +0 -54
- arviz/data/io_netcdf.py +0 -68
- arviz/data/io_numpyro.py +0 -497
- arviz/data/io_pyjags.py +0 -378
- arviz/data/io_pyro.py +0 -333
- arviz/data/io_pystan.py +0 -1095
- arviz/data/io_zarr.py +0 -46
- arviz/data/utils.py +0 -139
- arviz/labels.py +0 -210
- arviz/plots/__init__.py +0 -61
- arviz/plots/autocorrplot.py +0 -171
- arviz/plots/backends/__init__.py +0 -223
- arviz/plots/backends/bokeh/__init__.py +0 -166
- arviz/plots/backends/bokeh/autocorrplot.py +0 -101
- arviz/plots/backends/bokeh/bfplot.py +0 -23
- arviz/plots/backends/bokeh/bpvplot.py +0 -193
- arviz/plots/backends/bokeh/compareplot.py +0 -167
- arviz/plots/backends/bokeh/densityplot.py +0 -239
- arviz/plots/backends/bokeh/distcomparisonplot.py +0 -23
- arviz/plots/backends/bokeh/distplot.py +0 -183
- arviz/plots/backends/bokeh/dotplot.py +0 -113
- arviz/plots/backends/bokeh/ecdfplot.py +0 -73
- arviz/plots/backends/bokeh/elpdplot.py +0 -203
- arviz/plots/backends/bokeh/energyplot.py +0 -155
- arviz/plots/backends/bokeh/essplot.py +0 -176
- arviz/plots/backends/bokeh/forestplot.py +0 -772
- arviz/plots/backends/bokeh/hdiplot.py +0 -54
- arviz/plots/backends/bokeh/kdeplot.py +0 -268
- arviz/plots/backends/bokeh/khatplot.py +0 -163
- arviz/plots/backends/bokeh/lmplot.py +0 -185
- arviz/plots/backends/bokeh/loopitplot.py +0 -211
- arviz/plots/backends/bokeh/mcseplot.py +0 -184
- arviz/plots/backends/bokeh/pairplot.py +0 -328
- arviz/plots/backends/bokeh/parallelplot.py +0 -81
- arviz/plots/backends/bokeh/posteriorplot.py +0 -324
- arviz/plots/backends/bokeh/ppcplot.py +0 -379
- arviz/plots/backends/bokeh/rankplot.py +0 -149
- arviz/plots/backends/bokeh/separationplot.py +0 -107
- arviz/plots/backends/bokeh/traceplot.py +0 -436
- arviz/plots/backends/bokeh/violinplot.py +0 -164
- arviz/plots/backends/matplotlib/__init__.py +0 -124
- arviz/plots/backends/matplotlib/autocorrplot.py +0 -72
- arviz/plots/backends/matplotlib/bfplot.py +0 -78
- arviz/plots/backends/matplotlib/bpvplot.py +0 -177
- arviz/plots/backends/matplotlib/compareplot.py +0 -135
- arviz/plots/backends/matplotlib/densityplot.py +0 -194
- arviz/plots/backends/matplotlib/distcomparisonplot.py +0 -119
- arviz/plots/backends/matplotlib/distplot.py +0 -178
- arviz/plots/backends/matplotlib/dotplot.py +0 -116
- arviz/plots/backends/matplotlib/ecdfplot.py +0 -70
- arviz/plots/backends/matplotlib/elpdplot.py +0 -189
- arviz/plots/backends/matplotlib/energyplot.py +0 -113
- arviz/plots/backends/matplotlib/essplot.py +0 -180
- arviz/plots/backends/matplotlib/forestplot.py +0 -656
- arviz/plots/backends/matplotlib/hdiplot.py +0 -48
- arviz/plots/backends/matplotlib/kdeplot.py +0 -177
- arviz/plots/backends/matplotlib/khatplot.py +0 -241
- arviz/plots/backends/matplotlib/lmplot.py +0 -149
- arviz/plots/backends/matplotlib/loopitplot.py +0 -144
- arviz/plots/backends/matplotlib/mcseplot.py +0 -161
- arviz/plots/backends/matplotlib/pairplot.py +0 -355
- arviz/plots/backends/matplotlib/parallelplot.py +0 -58
- arviz/plots/backends/matplotlib/posteriorplot.py +0 -348
- arviz/plots/backends/matplotlib/ppcplot.py +0 -478
- arviz/plots/backends/matplotlib/rankplot.py +0 -119
- arviz/plots/backends/matplotlib/separationplot.py +0 -97
- arviz/plots/backends/matplotlib/traceplot.py +0 -526
- arviz/plots/backends/matplotlib/tsplot.py +0 -121
- arviz/plots/backends/matplotlib/violinplot.py +0 -148
- arviz/plots/bfplot.py +0 -128
- arviz/plots/bpvplot.py +0 -308
- arviz/plots/compareplot.py +0 -177
- arviz/plots/densityplot.py +0 -284
- arviz/plots/distcomparisonplot.py +0 -197
- arviz/plots/distplot.py +0 -233
- arviz/plots/dotplot.py +0 -233
- arviz/plots/ecdfplot.py +0 -372
- arviz/plots/elpdplot.py +0 -174
- arviz/plots/energyplot.py +0 -147
- arviz/plots/essplot.py +0 -319
- arviz/plots/forestplot.py +0 -304
- arviz/plots/hdiplot.py +0 -211
- arviz/plots/kdeplot.py +0 -357
- arviz/plots/khatplot.py +0 -236
- arviz/plots/lmplot.py +0 -380
- arviz/plots/loopitplot.py +0 -224
- arviz/plots/mcseplot.py +0 -194
- arviz/plots/pairplot.py +0 -281
- arviz/plots/parallelplot.py +0 -204
- arviz/plots/plot_utils.py +0 -599
- arviz/plots/posteriorplot.py +0 -298
- arviz/plots/ppcplot.py +0 -369
- arviz/plots/rankplot.py +0 -232
- arviz/plots/separationplot.py +0 -167
- arviz/plots/styles/arviz-bluish.mplstyle +0 -1
- arviz/plots/styles/arviz-brownish.mplstyle +0 -1
- arviz/plots/styles/arviz-colors.mplstyle +0 -2
- arviz/plots/styles/arviz-cyanish.mplstyle +0 -1
- arviz/plots/styles/arviz-darkgrid.mplstyle +0 -40
- arviz/plots/styles/arviz-doc.mplstyle +0 -88
- arviz/plots/styles/arviz-docgrid.mplstyle +0 -88
- arviz/plots/styles/arviz-grayscale.mplstyle +0 -41
- arviz/plots/styles/arviz-greenish.mplstyle +0 -1
- arviz/plots/styles/arviz-orangish.mplstyle +0 -1
- arviz/plots/styles/arviz-plasmish.mplstyle +0 -1
- arviz/plots/styles/arviz-purplish.mplstyle +0 -1
- arviz/plots/styles/arviz-redish.mplstyle +0 -1
- arviz/plots/styles/arviz-royish.mplstyle +0 -1
- arviz/plots/styles/arviz-viridish.mplstyle +0 -1
- arviz/plots/styles/arviz-white.mplstyle +0 -40
- arviz/plots/styles/arviz-whitegrid.mplstyle +0 -40
- arviz/plots/traceplot.py +0 -273
- arviz/plots/tsplot.py +0 -440
- arviz/plots/violinplot.py +0 -192
- arviz/preview.py +0 -58
- arviz/py.typed +0 -0
- arviz/rcparams.py +0 -606
- arviz/sel_utils.py +0 -223
- arviz/static/css/style.css +0 -340
- arviz/static/html/icons-svg-inline.html +0 -15
- arviz/stats/__init__.py +0 -37
- arviz/stats/density_utils.py +0 -1013
- arviz/stats/diagnostics.py +0 -1013
- arviz/stats/ecdf_utils.py +0 -324
- arviz/stats/stats.py +0 -2422
- arviz/stats/stats_refitting.py +0 -119
- arviz/stats/stats_utils.py +0 -609
- arviz/tests/__init__.py +0 -1
- arviz/tests/base_tests/__init__.py +0 -1
- arviz/tests/base_tests/test_data.py +0 -1679
- arviz/tests/base_tests/test_data_zarr.py +0 -143
- arviz/tests/base_tests/test_diagnostics.py +0 -511
- arviz/tests/base_tests/test_diagnostics_numba.py +0 -87
- arviz/tests/base_tests/test_helpers.py +0 -18
- arviz/tests/base_tests/test_labels.py +0 -69
- arviz/tests/base_tests/test_plot_utils.py +0 -342
- arviz/tests/base_tests/test_plots_bokeh.py +0 -1288
- arviz/tests/base_tests/test_plots_matplotlib.py +0 -2197
- arviz/tests/base_tests/test_rcparams.py +0 -317
- arviz/tests/base_tests/test_stats.py +0 -925
- arviz/tests/base_tests/test_stats_ecdf_utils.py +0 -166
- arviz/tests/base_tests/test_stats_numba.py +0 -45
- arviz/tests/base_tests/test_stats_utils.py +0 -384
- arviz/tests/base_tests/test_utils.py +0 -376
- arviz/tests/base_tests/test_utils_numba.py +0 -87
- arviz/tests/conftest.py +0 -46
- arviz/tests/external_tests/__init__.py +0 -1
- arviz/tests/external_tests/test_data_beanmachine.py +0 -78
- arviz/tests/external_tests/test_data_cmdstan.py +0 -398
- arviz/tests/external_tests/test_data_cmdstanpy.py +0 -496
- arviz/tests/external_tests/test_data_emcee.py +0 -166
- arviz/tests/external_tests/test_data_numpyro.py +0 -434
- arviz/tests/external_tests/test_data_pyjags.py +0 -119
- arviz/tests/external_tests/test_data_pyro.py +0 -260
- arviz/tests/external_tests/test_data_pystan.py +0 -307
- arviz/tests/helpers.py +0 -677
- arviz/utils.py +0 -773
- arviz/wrappers/__init__.py +0 -13
- arviz/wrappers/base.py +0 -236
- arviz/wrappers/wrap_pymc.py +0 -36
- arviz/wrappers/wrap_stan.py +0 -148
- arviz-0.23.3.dist-info/METADATA +0 -264
- arviz-0.23.3.dist-info/RECORD +0 -183
- arviz-0.23.3.dist-info/top_level.txt +0 -1
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"""Matplotlib loopitplot."""
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import matplotlib.pyplot as plt
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import numpy as np
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from matplotlib.colors import hsv_to_rgb, rgb_to_hsv, to_hex, to_rgb
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from xarray import DataArray
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from ....stats.density_utils import kde
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from ...plot_utils import _scale_fig_size
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from . import backend_kwarg_defaults, backend_show, create_axes_grid, matplotlib_kwarg_dealiaser
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def plot_loo_pit(
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ax,
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figsize,
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ecdf,
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loo_pit,
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loo_pit_ecdf,
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unif_ecdf,
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p975,
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p025,
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fill_kwargs,
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ecdf_fill,
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x_vals,
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hdi_kwargs,
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hdi_odds,
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unif,
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plot_unif_kwargs,
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loo_pit_kde,
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legend,
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labeller,
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y,
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color,
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textsize,
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plot_kwargs,
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show,
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):
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"""Matplotlib loo pit plot."""
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backend_kwargs = {}
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backend_kwargs = {
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**backend_kwarg_defaults(),
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**backend_kwargs,
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}
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(figsize, _, _, xt_labelsize, linewidth, _) = _scale_fig_size(figsize, textsize, 1, 1)
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backend_kwargs.setdefault("figsize", figsize)
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plot_kwargs = matplotlib_kwarg_dealiaser(plot_kwargs, "plot")
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plot_kwargs["color"] = to_hex(color)
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plot_kwargs.setdefault("linewidth", linewidth * 1.4)
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if isinstance(y, str):
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plot_unif_kwargs.setdefault("color", to_hex(hsv_to_rgb(light_color)))
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ax.plot(
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ax.fill_between(unif_ecdf, p975 - unif_ecdf, p025 - unif_ecdf, **fill_kwargs)
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ax.plot(unif_ecdf, p975 - unif_ecdf, unif_ecdf, p025 - unif_ecdf, **plot_unif_kwargs)
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x_ss = np.empty((n_unif, len(loo_pit_kde)))
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ax.axhspan(*hdi_odds, **hdi_kwargs)
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ax.axhline(1, color="w", zorder=1)
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x_s, unif_density = kde(unif[idx, :])
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x_ss[idx] = x_s
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u_dens[idx] = unif_density
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ax.plot(x_ss.T, u_dens.T, **plot_unif_kwargs)
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ax.plot(x_vals, loo_pit_kde, **plot_kwargs)
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ax.set_ylim(0, None)
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if not (use_hdi or (ecdf and ecdf_fill)):
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label = f"{hdi_prob * 100:.3g}% credible interval" if ecdf else "Uniform"
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ax.plot([], label=label, **plot_unif_kwargs)
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ax.legend()
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from ....stats.stats_utils import quantile as _quantile
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from ...plot_utils import _scale_fig_size
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from . import backend_kwarg_defaults, backend_show, create_axes_grid, matplotlib_kwarg_dealiaser
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def plot_mcse(
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ax,
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plotters,
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length_plotters,
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rows,
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cols,
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figsize,
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errorbar,
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rug,
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data,
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probs,
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kwargs,
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extra_methods,
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mean_mcse,
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sd_mcse,
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textsize,
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labeller,
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text_kwargs,
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rug_kwargs,
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extra_kwargs,
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idata,
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rug_kind,
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backend_kwargs,
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show,
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):
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"""Matplotlib mcseplot."""
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if backend_kwargs is None:
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backend_kwargs = {}
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backend_kwargs = {
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**backend_kwarg_defaults(),
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**backend_kwargs,
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}
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(figsize, ax_labelsize, titlesize, xt_labelsize, _linewidth, _markersize) = _scale_fig_size(
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figsize, textsize, rows, cols
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)
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backend_kwargs.setdefault("figsize", figsize)
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backend_kwargs["squeeze"] = True
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kwargs = matplotlib_kwarg_dealiaser(kwargs, "plot")
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kwargs.setdefault("linestyle", "none")
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kwargs.setdefault("linewidth", _linewidth)
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kwargs.setdefault("markersize", _markersize)
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kwargs.setdefault("marker", "_" if errorbar else "o")
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kwargs.setdefault("zorder", 3)
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extra_kwargs = matplotlib_kwarg_dealiaser(extra_kwargs, "plot")
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extra_kwargs.setdefault("linestyle", "-")
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extra_kwargs.setdefault("linewidth", _linewidth / 2)
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extra_kwargs.setdefault("color", "k")
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extra_kwargs.setdefault("alpha", 0.5)
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text_x = None
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text_va = None
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if extra_methods:
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text_kwargs = matplotlib_kwarg_dealiaser(text_kwargs, "text")
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text_x = text_kwargs.pop("x", 1)
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text_kwargs.setdefault("fontsize", xt_labelsize * 0.7)
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text_kwargs.setdefault("alpha", extra_kwargs["alpha"])
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text_kwargs.setdefault("color", extra_kwargs["color"])
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text_kwargs.setdefault("horizontalalignment", "right")
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text_va = text_kwargs.pop("verticalalignment", None)
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if ax is None:
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_, ax = create_axes_grid(
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length_plotters,
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rows,
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cols,
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backend_kwargs=backend_kwargs,
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)
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for (var_name, selection, isel, x), ax_ in zip(plotters, np.ravel(ax)):
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if errorbar or rug:
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values = data[var_name].sel(**selection).values.flatten()
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if errorbar:
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quantile_values = _quantile(values, probs)
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ax_.errorbar(probs, quantile_values, yerr=x, **kwargs)
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else:
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ax_.plot(probs, x, label="quantile", **kwargs)
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if extra_methods:
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mean_mcse_i = mean_mcse[var_name].sel(**selection).values.item()
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sd_mcse_i = sd_mcse[var_name].sel(**selection).values.item()
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ax_.axhline(mean_mcse_i, **extra_kwargs)
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ax_.annotate(
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"mean",
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(text_x, mean_mcse_i),
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va=(
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text_va
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if text_va is not None
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else "bottom" if mean_mcse_i > sd_mcse_i else "top"
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),
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**text_kwargs,
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)
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ax_.axhline(sd_mcse_i, **extra_kwargs)
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ax_.annotate(
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"sd",
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(text_x, sd_mcse_i),
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va=(
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text_va
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if text_va is not None
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else "bottom" if sd_mcse_i >= mean_mcse_i else "top"
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),
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**text_kwargs,
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)
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if rug:
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rug_kwargs = matplotlib_kwarg_dealiaser(rug_kwargs, "plot")
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if not hasattr(idata, "sample_stats"):
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raise ValueError("InferenceData object must contain sample_stats for rug plot")
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if not hasattr(idata.sample_stats, rug_kind):
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raise ValueError(f"InferenceData does not contain {rug_kind} data")
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rug_kwargs.setdefault("marker", "|")
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rug_kwargs.setdefault("linestyle", rug_kwargs.pop("ls", "None"))
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rug_kwargs.setdefault("color", rug_kwargs.pop("c", kwargs.get("color", "C0")))
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rug_kwargs.setdefault("space", 0.1)
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rug_kwargs.setdefault("markersize", rug_kwargs.pop("ms", 2 * _markersize))
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|
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mask = idata.sample_stats[rug_kind].values.flatten()
|
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values = rankdata(values, method="average")[mask]
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|
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y_min, y_max = ax_.get_ylim()
|
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y_min = y_min if errorbar else 0
|
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rug_space = (y_max - y_min) * rug_kwargs.pop("space")
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rug_x, rug_y = values / (len(mask) - 1), np.full_like(values, y_min) - rug_space
|
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ax_.plot(rug_x, rug_y, **rug_kwargs)
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ax_.axhline(y_min, color="k", linewidth=_linewidth, alpha=0.7)
|
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|
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|
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ax_.set_title(
|
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labeller.make_label_vert(var_name, selection, isel), fontsize=titlesize, wrap=True
|
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|
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)
|
|
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|
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ax_.tick_params(labelsize=xt_labelsize)
|
|
141
|
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ax_.set_xlabel("Quantile", fontsize=ax_labelsize, wrap=True)
|
|
142
|
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ax_.set_ylabel(
|
|
143
|
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r"Value $\pm$ MCSE for quantiles" if errorbar else "MCSE for quantiles",
|
|
144
|
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fontsize=ax_labelsize,
|
|
145
|
-
wrap=True,
|
|
146
|
-
)
|
|
147
|
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ax_.set_xlim(0, 1)
|
|
148
|
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if rug:
|
|
149
|
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ax_.yaxis.get_major_locator().set_params(nbins="auto", steps=[1, 2, 5, 10])
|
|
150
|
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y_min, y_max = ax_.get_ylim()
|
|
151
|
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yticks = ax_.get_yticks()
|
|
152
|
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yticks = yticks[(yticks >= y_min) & (yticks < y_max)]
|
|
153
|
-
ax_.set_yticks(yticks)
|
|
154
|
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ax_.set_yticklabels([f"{ytick:.3g}" for ytick in yticks])
|
|
155
|
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elif not errorbar:
|
|
156
|
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ax_.set_ylim(bottom=0)
|
|
157
|
-
|
|
158
|
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if backend_show(show):
|
|
159
|
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plt.show()
|
|
160
|
-
|
|
161
|
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return ax
|
|
@@ -1,355 +0,0 @@
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1
|
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"""Matplotlib pairplot."""
|
|
2
|
-
|
|
3
|
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import warnings
|
|
4
|
-
from copy import deepcopy
|
|
5
|
-
|
|
6
|
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import matplotlib.pyplot as plt
|
|
7
|
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import numpy as np
|
|
8
|
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from mpl_toolkits.axes_grid1 import make_axes_locatable
|
|
9
|
-
|
|
10
|
-
from ....rcparams import rcParams
|
|
11
|
-
from ...distplot import plot_dist
|
|
12
|
-
from ...kdeplot import plot_kde
|
|
13
|
-
from ...plot_utils import _scale_fig_size, calculate_point_estimate, _init_kwargs_dict
|
|
14
|
-
from . import backend_kwarg_defaults, backend_show, matplotlib_kwarg_dealiaser
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
def plot_pair(
|
|
18
|
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ax,
|
|
19
|
-
plotters,
|
|
20
|
-
numvars,
|
|
21
|
-
figsize,
|
|
22
|
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textsize,
|
|
23
|
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kind,
|
|
24
|
-
scatter_kwargs,
|
|
25
|
-
kde_kwargs,
|
|
26
|
-
hexbin_kwargs,
|
|
27
|
-
gridsize,
|
|
28
|
-
colorbar,
|
|
29
|
-
divergences,
|
|
30
|
-
diverging_mask,
|
|
31
|
-
divergences_kwargs,
|
|
32
|
-
flat_var_names,
|
|
33
|
-
flat_ref_slices,
|
|
34
|
-
flat_var_labels,
|
|
35
|
-
backend_kwargs,
|
|
36
|
-
marginal_kwargs,
|
|
37
|
-
show,
|
|
38
|
-
marginals,
|
|
39
|
-
point_estimate,
|
|
40
|
-
point_estimate_kwargs,
|
|
41
|
-
point_estimate_marker_kwargs,
|
|
42
|
-
reference_values,
|
|
43
|
-
reference_values_kwargs,
|
|
44
|
-
):
|
|
45
|
-
"""Matplotlib pairplot."""
|
|
46
|
-
backend_kwargs = _init_kwargs_dict(backend_kwargs)
|
|
47
|
-
backend_kwargs = {
|
|
48
|
-
**backend_kwarg_defaults(),
|
|
49
|
-
**backend_kwargs,
|
|
50
|
-
}
|
|
51
|
-
|
|
52
|
-
scatter_kwargs = matplotlib_kwarg_dealiaser(scatter_kwargs, "scatter")
|
|
53
|
-
|
|
54
|
-
scatter_kwargs.setdefault("marker", ".")
|
|
55
|
-
scatter_kwargs.setdefault("lw", 0)
|
|
56
|
-
# Sets the default zorder higher than zorder of grid, which is 0.5
|
|
57
|
-
scatter_kwargs.setdefault("zorder", 0.6)
|
|
58
|
-
|
|
59
|
-
kde_kwargs = _init_kwargs_dict(kde_kwargs)
|
|
60
|
-
|
|
61
|
-
hexbin_kwargs = matplotlib_kwarg_dealiaser(hexbin_kwargs, "hexbin")
|
|
62
|
-
hexbin_kwargs.setdefault("mincnt", 1)
|
|
63
|
-
|
|
64
|
-
divergences_kwargs = matplotlib_kwarg_dealiaser(divergences_kwargs, "plot")
|
|
65
|
-
divergences_kwargs.setdefault("marker", "o")
|
|
66
|
-
divergences_kwargs.setdefault("markeredgecolor", "k")
|
|
67
|
-
divergences_kwargs.setdefault("color", "C1")
|
|
68
|
-
divergences_kwargs.setdefault("lw", 0)
|
|
69
|
-
|
|
70
|
-
marginal_kwargs = _init_kwargs_dict(marginal_kwargs)
|
|
71
|
-
|
|
72
|
-
point_estimate_kwargs = matplotlib_kwarg_dealiaser(point_estimate_kwargs, "fill_between")
|
|
73
|
-
point_estimate_kwargs.setdefault("color", "k")
|
|
74
|
-
|
|
75
|
-
if kind != "kde":
|
|
76
|
-
kde_kwargs.setdefault("contourf_kwargs", {})
|
|
77
|
-
kde_kwargs["contourf_kwargs"].setdefault("alpha", 0)
|
|
78
|
-
kde_kwargs.setdefault("contour_kwargs", {})
|
|
79
|
-
kde_kwargs["contour_kwargs"].setdefault("colors", "k")
|
|
80
|
-
|
|
81
|
-
if reference_values:
|
|
82
|
-
difference = set(flat_var_names).difference(set(reference_values.keys()))
|
|
83
|
-
|
|
84
|
-
if difference:
|
|
85
|
-
warnings.warn(
|
|
86
|
-
"Argument reference_values does not include reference value for: {}".format(
|
|
87
|
-
", ".join(difference)
|
|
88
|
-
),
|
|
89
|
-
UserWarning,
|
|
90
|
-
)
|
|
91
|
-
|
|
92
|
-
reference_values_kwargs = matplotlib_kwarg_dealiaser(reference_values_kwargs, "plot")
|
|
93
|
-
|
|
94
|
-
reference_values_kwargs.setdefault("color", "C2")
|
|
95
|
-
reference_values_kwargs.setdefault("markeredgecolor", "k")
|
|
96
|
-
reference_values_kwargs.setdefault("marker", "o")
|
|
97
|
-
|
|
98
|
-
point_estimate_marker_kwargs = matplotlib_kwarg_dealiaser(
|
|
99
|
-
point_estimate_marker_kwargs, "scatter"
|
|
100
|
-
)
|
|
101
|
-
point_estimate_marker_kwargs.setdefault("marker", "s")
|
|
102
|
-
point_estimate_marker_kwargs.setdefault("color", "k")
|
|
103
|
-
|
|
104
|
-
# pylint: disable=too-many-nested-blocks
|
|
105
|
-
if numvars == 2:
|
|
106
|
-
(figsize, ax_labelsize, _, xt_labelsize, linewidth, markersize) = _scale_fig_size(
|
|
107
|
-
figsize, textsize, numvars - 1, numvars - 1
|
|
108
|
-
)
|
|
109
|
-
backend_kwargs.setdefault("figsize", figsize)
|
|
110
|
-
|
|
111
|
-
marginal_kwargs.setdefault("plot_kwargs", {})
|
|
112
|
-
marginal_kwargs["plot_kwargs"].setdefault("linewidth", linewidth)
|
|
113
|
-
|
|
114
|
-
point_estimate_marker_kwargs.setdefault("s", markersize + 50)
|
|
115
|
-
|
|
116
|
-
# Flatten data
|
|
117
|
-
x = plotters[0][-1].flatten()
|
|
118
|
-
y = plotters[1][-1].flatten()
|
|
119
|
-
if ax is None:
|
|
120
|
-
if marginals:
|
|
121
|
-
# Instantiate figure and grid
|
|
122
|
-
widths = [2, 2, 2, 1]
|
|
123
|
-
heights = [1.4, 2, 2, 2]
|
|
124
|
-
fig = plt.figure(**backend_kwargs)
|
|
125
|
-
grid = plt.GridSpec(
|
|
126
|
-
4,
|
|
127
|
-
4,
|
|
128
|
-
hspace=0.1,
|
|
129
|
-
wspace=0.1,
|
|
130
|
-
figure=fig,
|
|
131
|
-
width_ratios=widths,
|
|
132
|
-
height_ratios=heights,
|
|
133
|
-
)
|
|
134
|
-
# Set up main plot
|
|
135
|
-
ax = fig.add_subplot(grid[1:, :-1])
|
|
136
|
-
# Set up top KDE
|
|
137
|
-
ax_hist_x = fig.add_subplot(grid[0, :-1], sharex=ax)
|
|
138
|
-
ax_hist_x.set_yticks([])
|
|
139
|
-
# Set up right KDE
|
|
140
|
-
ax_hist_y = fig.add_subplot(grid[1:, -1], sharey=ax)
|
|
141
|
-
ax_hist_y.set_xticks([])
|
|
142
|
-
ax_return = np.array([[ax_hist_x, None], [ax, ax_hist_y]])
|
|
143
|
-
|
|
144
|
-
for val, ax_, rotate in ((x, ax_hist_x, False), (y, ax_hist_y, True)):
|
|
145
|
-
plot_dist(val, textsize=xt_labelsize, rotated=rotate, ax=ax_, **marginal_kwargs)
|
|
146
|
-
|
|
147
|
-
# Personalize axes
|
|
148
|
-
ax_hist_x.tick_params(labelleft=False, labelbottom=False)
|
|
149
|
-
ax_hist_y.tick_params(labelleft=False, labelbottom=False)
|
|
150
|
-
else:
|
|
151
|
-
fig, ax = plt.subplots(numvars - 1, numvars - 1, **backend_kwargs)
|
|
152
|
-
else:
|
|
153
|
-
if marginals:
|
|
154
|
-
assert ax.shape == (numvars, numvars)
|
|
155
|
-
if ax[0, 1] is not None and ax[0, 1].get_figure() is not None:
|
|
156
|
-
ax[0, 1].remove()
|
|
157
|
-
ax_return = ax
|
|
158
|
-
ax_hist_x = ax[0, 0]
|
|
159
|
-
ax_hist_y = ax[1, 1]
|
|
160
|
-
ax = ax[1, 0]
|
|
161
|
-
for val, ax_, rotate in ((x, ax_hist_x, False), (y, ax_hist_y, True)):
|
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162
|
-
plot_dist(val, textsize=xt_labelsize, rotated=rotate, ax=ax_, **marginal_kwargs)
|
|
163
|
-
else:
|
|
164
|
-
ax = np.atleast_2d(ax)[0, 0]
|
|
165
|
-
|
|
166
|
-
if "scatter" in kind:
|
|
167
|
-
ax.scatter(x, y, **scatter_kwargs)
|
|
168
|
-
if "kde" in kind:
|
|
169
|
-
plot_kde(x, y, ax=ax, **kde_kwargs)
|
|
170
|
-
if "hexbin" in kind:
|
|
171
|
-
hexbin = ax.hexbin(
|
|
172
|
-
x,
|
|
173
|
-
y,
|
|
174
|
-
gridsize=gridsize,
|
|
175
|
-
**hexbin_kwargs,
|
|
176
|
-
)
|
|
177
|
-
ax.grid(False)
|
|
178
|
-
|
|
179
|
-
if kind == "hexbin" and colorbar:
|
|
180
|
-
cbar = ax.figure.colorbar(hexbin, ticks=[hexbin.norm.vmin, hexbin.norm.vmax], ax=ax)
|
|
181
|
-
cbar.ax.set_yticklabels(["low", "high"], fontsize=ax_labelsize)
|
|
182
|
-
|
|
183
|
-
if divergences:
|
|
184
|
-
ax.plot(
|
|
185
|
-
x[diverging_mask],
|
|
186
|
-
y[diverging_mask],
|
|
187
|
-
**divergences_kwargs,
|
|
188
|
-
)
|
|
189
|
-
|
|
190
|
-
if point_estimate:
|
|
191
|
-
pe_x = calculate_point_estimate(point_estimate, x)
|
|
192
|
-
pe_y = calculate_point_estimate(point_estimate, y)
|
|
193
|
-
if marginals:
|
|
194
|
-
ax_hist_x.axvline(pe_x, **point_estimate_kwargs)
|
|
195
|
-
ax_hist_y.axhline(pe_y, **point_estimate_kwargs)
|
|
196
|
-
|
|
197
|
-
ax.axvline(pe_x, **point_estimate_kwargs)
|
|
198
|
-
ax.axhline(pe_y, **point_estimate_kwargs)
|
|
199
|
-
|
|
200
|
-
ax.scatter(pe_x, pe_y, **point_estimate_marker_kwargs)
|
|
201
|
-
|
|
202
|
-
if reference_values:
|
|
203
|
-
ax.plot(
|
|
204
|
-
np.array(reference_values[flat_var_names[0]])[flat_ref_slices[0]],
|
|
205
|
-
np.array(reference_values[flat_var_names[1]])[flat_ref_slices[1]],
|
|
206
|
-
**reference_values_kwargs,
|
|
207
|
-
)
|
|
208
|
-
ax.set_xlabel(f"{flat_var_labels[0]}", fontsize=ax_labelsize, wrap=True)
|
|
209
|
-
ax.set_ylabel(f"{flat_var_labels[1]}", fontsize=ax_labelsize, wrap=True)
|
|
210
|
-
ax.tick_params(labelsize=xt_labelsize)
|
|
211
|
-
|
|
212
|
-
else:
|
|
213
|
-
not_marginals = int(not marginals)
|
|
214
|
-
num_subplot_cols = numvars - not_marginals
|
|
215
|
-
max_plots = (
|
|
216
|
-
num_subplot_cols**2
|
|
217
|
-
if rcParams["plot.max_subplots"] is None
|
|
218
|
-
else rcParams["plot.max_subplots"]
|
|
219
|
-
)
|
|
220
|
-
cols_to_plot = np.sum(np.arange(1, num_subplot_cols + 1).cumsum() <= max_plots)
|
|
221
|
-
if cols_to_plot < num_subplot_cols:
|
|
222
|
-
vars_to_plot = cols_to_plot
|
|
223
|
-
warnings.warn(
|
|
224
|
-
"rcParams['plot.max_subplots'] ({max_plots}) is smaller than the number "
|
|
225
|
-
"of resulting pair plots with these variables, generating only a "
|
|
226
|
-
"{side}x{side} grid".format(max_plots=max_plots, side=vars_to_plot),
|
|
227
|
-
UserWarning,
|
|
228
|
-
)
|
|
229
|
-
else:
|
|
230
|
-
vars_to_plot = numvars - not_marginals
|
|
231
|
-
|
|
232
|
-
(figsize, ax_labelsize, _, xt_labelsize, _, markersize) = _scale_fig_size(
|
|
233
|
-
figsize, textsize, vars_to_plot, vars_to_plot
|
|
234
|
-
)
|
|
235
|
-
backend_kwargs.setdefault("figsize", figsize)
|
|
236
|
-
point_estimate_marker_kwargs.setdefault("s", markersize + 50)
|
|
237
|
-
|
|
238
|
-
if ax is None:
|
|
239
|
-
if backend_kwargs.pop("sharex", None) is not None:
|
|
240
|
-
warnings.warn(
|
|
241
|
-
"'sharex' keyword is ignored. For non-standard sharing, provide 'ax'.",
|
|
242
|
-
UserWarning,
|
|
243
|
-
)
|
|
244
|
-
if backend_kwargs.pop("sharey", None) is not None:
|
|
245
|
-
warnings.warn(
|
|
246
|
-
"'sharey' keyword is ignored. For non-standard sharing, provide 'ax'.",
|
|
247
|
-
UserWarning,
|
|
248
|
-
)
|
|
249
|
-
backend_kwargs["sharex"] = "col"
|
|
250
|
-
if not_marginals:
|
|
251
|
-
backend_kwargs["sharey"] = "row"
|
|
252
|
-
fig, ax = plt.subplots(
|
|
253
|
-
vars_to_plot,
|
|
254
|
-
vars_to_plot,
|
|
255
|
-
**backend_kwargs,
|
|
256
|
-
)
|
|
257
|
-
if backend_kwargs.get("sharey") is None:
|
|
258
|
-
for j in range(0, vars_to_plot):
|
|
259
|
-
for i in range(0, j):
|
|
260
|
-
ax[j, i].axes.sharey(ax[j, 0])
|
|
261
|
-
|
|
262
|
-
hexbin_values = []
|
|
263
|
-
for i in range(0, vars_to_plot):
|
|
264
|
-
var1 = plotters[i][-1].flatten()
|
|
265
|
-
|
|
266
|
-
for j in range(0, vars_to_plot):
|
|
267
|
-
var2 = plotters[j + not_marginals][-1].flatten()
|
|
268
|
-
if i > j:
|
|
269
|
-
if ax[j, i].get_figure() is not None:
|
|
270
|
-
ax[j, i].remove()
|
|
271
|
-
continue
|
|
272
|
-
|
|
273
|
-
elif i == j and marginals:
|
|
274
|
-
loc = "right"
|
|
275
|
-
plot_dist(var1, ax=ax[i, j], **marginal_kwargs)
|
|
276
|
-
|
|
277
|
-
else:
|
|
278
|
-
if i == j:
|
|
279
|
-
loc = "left"
|
|
280
|
-
|
|
281
|
-
if "scatter" in kind:
|
|
282
|
-
ax[j, i].scatter(var1, var2, **scatter_kwargs)
|
|
283
|
-
|
|
284
|
-
if "kde" in kind:
|
|
285
|
-
plot_kde(
|
|
286
|
-
var1,
|
|
287
|
-
var2,
|
|
288
|
-
ax=ax[j, i],
|
|
289
|
-
**deepcopy(kde_kwargs),
|
|
290
|
-
)
|
|
291
|
-
|
|
292
|
-
if "hexbin" in kind:
|
|
293
|
-
ax[j, i].grid(False)
|
|
294
|
-
hexbin = ax[j, i].hexbin(var1, var2, gridsize=gridsize, **hexbin_kwargs)
|
|
295
|
-
|
|
296
|
-
if divergences:
|
|
297
|
-
ax[j, i].plot(
|
|
298
|
-
var1[diverging_mask], var2[diverging_mask], **divergences_kwargs
|
|
299
|
-
)
|
|
300
|
-
|
|
301
|
-
if kind == "hexbin" and colorbar:
|
|
302
|
-
hexbin_values.append(hexbin.norm.vmin)
|
|
303
|
-
hexbin_values.append(hexbin.norm.vmax)
|
|
304
|
-
divider = make_axes_locatable(ax[-1, -1])
|
|
305
|
-
cax = divider.append_axes(loc, size="7%", pad="5%")
|
|
306
|
-
cbar = fig.colorbar(
|
|
307
|
-
hexbin, ticks=[hexbin.norm.vmin, hexbin.norm.vmax], cax=cax
|
|
308
|
-
)
|
|
309
|
-
cbar.ax.set_yticklabels(["low", "high"], fontsize=ax_labelsize)
|
|
310
|
-
|
|
311
|
-
if point_estimate:
|
|
312
|
-
pe_x = calculate_point_estimate(point_estimate, var1)
|
|
313
|
-
pe_y = calculate_point_estimate(point_estimate, var2)
|
|
314
|
-
ax[j, i].axvline(pe_x, **point_estimate_kwargs)
|
|
315
|
-
ax[j, i].axhline(pe_y, **point_estimate_kwargs)
|
|
316
|
-
|
|
317
|
-
if marginals:
|
|
318
|
-
ax[j - 1, i].axvline(pe_x, **point_estimate_kwargs)
|
|
319
|
-
pe_last = calculate_point_estimate(point_estimate, plotters[-1][-1])
|
|
320
|
-
ax[-1, -1].axvline(pe_last, **point_estimate_kwargs)
|
|
321
|
-
|
|
322
|
-
ax[j, i].scatter(pe_x, pe_y, **point_estimate_marker_kwargs)
|
|
323
|
-
|
|
324
|
-
if reference_values:
|
|
325
|
-
x_name = flat_var_names[i]
|
|
326
|
-
y_name = flat_var_names[j + not_marginals]
|
|
327
|
-
if (x_name not in difference) and (y_name not in difference):
|
|
328
|
-
ax[j, i].plot(
|
|
329
|
-
np.array(reference_values[x_name])[flat_ref_slices[i]],
|
|
330
|
-
np.array(reference_values[y_name])[
|
|
331
|
-
flat_ref_slices[j + not_marginals]
|
|
332
|
-
],
|
|
333
|
-
**reference_values_kwargs,
|
|
334
|
-
)
|
|
335
|
-
|
|
336
|
-
if j != vars_to_plot - 1:
|
|
337
|
-
plt.setp(ax[j, i].get_xticklabels(), visible=False)
|
|
338
|
-
else:
|
|
339
|
-
ax[j, i].set_xlabel(f"{flat_var_labels[i]}", fontsize=ax_labelsize, wrap=True)
|
|
340
|
-
if i != 0:
|
|
341
|
-
plt.setp(ax[j, i].get_yticklabels(), visible=False)
|
|
342
|
-
else:
|
|
343
|
-
ax[j, i].set_ylabel(
|
|
344
|
-
f"{flat_var_labels[j + not_marginals]}",
|
|
345
|
-
fontsize=ax_labelsize,
|
|
346
|
-
wrap=True,
|
|
347
|
-
)
|
|
348
|
-
ax[j, i].tick_params(labelsize=xt_labelsize)
|
|
349
|
-
|
|
350
|
-
if backend_show(show):
|
|
351
|
-
plt.show()
|
|
352
|
-
|
|
353
|
-
if marginals and numvars == 2:
|
|
354
|
-
return ax_return
|
|
355
|
-
return ax
|