11836306515

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morganjwilliams

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Update example notebook

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/pyrolite/plot/__init__.py

"""
Submodule with various plotting and visualisation functions.
"""

import warnings

import matplotlib
import matplotlib.pyplot as plt
import mpltern
import numpy as np
import pandas as pd

warnings.filterwarnings("ignore", "Unknown section")

from .. import geochem
from ..comp.codata import ILR, close
from ..util.distributions import get_scaler, sample_kde
from ..util.log import Handle
from ..util.meta import get_additional_params, subkwargs
from ..util.pd import to_frame, _check_components
from ..util.plot.axes import init_axes, label_axes
from ..util.plot.helpers import plot_cooccurence
from ..util.plot.style import _export_nonRCstyles, linekwargs, scatterkwargs
from . import density, parallel, spider, stem
from .color import process_color

logger = Handle(__name__)

# pyroplot added to __all__ for docs
__all__ = ["density", "spider", "pyroplot"]


class pyroplot_matplotlib(object):
    def __init__(self, obj):
        """
        Custom dataframe accessor for pyrolite plotting.

        Notes
        -----
            This accessor enables the coexistence of array-based plotting functions and
            methods for pandas objects. This enables some separation of concerns.
        """
        self._validate(obj)
        self._obj = obj

        # refresh custom styling on creation?
        _export_nonRCstyles()

    @staticmethod
    def _validate(obj):
        pass

    def cooccurence(self, ax=None, normalize=True, log=False, colorbar=False, **kwargs):
        """
        Plot the co-occurence frequency matrix for a given input.

        Parameters
        ----------
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        normalize : :class:`bool`
            Whether to normalize the cooccurence to compare disparate variables.
        log : :class:`bool`
            Whether to take the log of the cooccurence.
        colorbar : :class:`bool`
            Whether to append a colorbar.

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the cooccurence plot is added.

        """
        obj = to_frame(self._obj)
        ax = plot_cooccurence(
            obj.values, ax=ax, normalize=normalize, log=log, colorbar=colorbar, **kwargs
        )
        ax.set_xticklabels(obj.columns, minor=False, rotation=90)
        ax.set_yticklabels(obj.columns, minor=False)
        return ax

    def density(self, components: list = None, ax=None, axlabels=True, **kwargs):
        r"""
        Method for plotting histograms (mode='hist2d'|'hexbin') or kernel density
        esitimates from point data. Convenience access function to
        :func:`~pyrolite.plot.density.density` (see `Other Parameters`, below), where
        further parameters for relevant `matplotlib` functions are also listed.

        Parameters
        ----------
        components : :class:`list`, :code:`None`
            Elements or compositional components to plot.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        axlabels : :class:`bool`, True
            Whether to add x-y axis labels.

        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the density diagram is plotted.

        """
        obj = to_frame(self._obj)
        components = _check_components(obj, components=components)

        ax = density.density(
            obj.reindex(columns=components).astype(float).values, ax=ax, **kwargs
        )
        if axlabels:
            label_axes(ax, labels=components)

        return ax

    def heatscatter(
        self,
        components: list = None,
        ax=None,
        axlabels=True,
        logx=False,
        logy=False,
        **kwargs,
    ):
        r"""
        Heatmapped scatter plots using the pyroplot API. See further parameters
        for `matplotlib.pyplot.scatter` function below.

        Parameters
        ----------
        components : :class:`list`, :code:`None`
            Elements or compositional components to plot.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        axlabels : :class:`bool`, :code:`True`
            Whether to add x-y axis labels.
        logx : :class:`bool`, `False`
            Whether to log-transform x values before the KDE for bivariate plots.
        logy : :class:`bool`, `False`
            Whether to log-transform y values before the KDE for bivariate plots.

        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the heatmapped scatterplot is added.

        """
        obj = to_frame(self._obj)
        components = _check_components(obj, components=components)
        data, samples = (
            obj.reindex(columns=components).values,
            obj.reindex(columns=components).values,
        )
        kdetfm = [  # log transforms
            get_scaler([None, np.log][logx], [None, np.log][logy]),
            lambda x: ILR(close(x)),
        ][len(components) == 3]
        zi = sample_kde(
            data, samples, transform=kdetfm, **subkwargs(kwargs, sample_kde)
        )
        kwargs.update({"c": zi})
        ax = obj.reindex(columns=components).pyroplot.scatter(
            ax=ax, axlabels=axlabels, **kwargs
        )
        return ax

    def parallel(
        self,
        components=None,
        rescale=False,
        legend=False,
        ax=None,
        **kwargs,
    ):
        """
        Create a :func:`pyrolite.plot.parallel.parallel`. coordinate plot from
        the columns of the :class:`~pandas.DataFrame`.

        Parameters
        ----------
        components : :class:`list`, :code:`None`
            Components to use as axes for the plot.
        rescale : :class:`bool`
            Whether to rescale values to [-1, 1].
        legend : :class:`bool`, :code:`False`
            Whether to include or suppress the legend.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the parallel coordinates plot is added.

        Todo
        ----
        * Adapt figure size based on number of columns.

        """

        obj = to_frame(self._obj)
        ax = parallel.parallel(
            obj,
            components=components,
            rescale=rescale,
            legend=legend,
            ax=ax,
            **kwargs,
        )
        return ax

    def plot(self, components: list = None, ax=None, axlabels=True, **kwargs):
        r"""
        Convenience method for line plots using the pyroplot API. See
        further parameters for `matplotlib.pyplot.scatter` function below.

        Parameters
        ----------
        components : :class:`list`, :code:`None`
            Elements or compositional components to plot.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        axlabels : :class:`bool`, :code:`True`
            Whether to add x-y axis labels.
        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the plot is added.

        """
        obj = to_frame(self._obj)
        components = _check_components(obj, components=components)
        projection = [None, "ternary"][len(components) == 3]
        ax = init_axes(ax=ax, projection=projection, **kwargs)
        kw = linekwargs(kwargs)
        ax.plot(*obj.reindex(columns=components).values.T, **kw)
        # if color is multi, could update line colors here
        if axlabels:
            label_axes(ax, labels=components)

        ax.tick_params("both")
        # ax.grid()
        # ax.set_aspect("equal")
        return ax

    def REE(
        self,
        index="elements",
        ax=None,
        mode="plot",
        dropPm=True,
        scatter_kw={},
        line_kw={},
        **kwargs,
    ):
        """Pass the pandas object to :func:`pyrolite.plot.spider.REE_v_radii`.

        Parameters
        ----------
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        index : :class:`str`
            Whether to plot radii ('radii') on the principal x-axis, or elements
            ('elements').
        mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
            Mode for plot. Plot will produce a line-scatter diagram. Fill will return
            a filled range. Density will return a conditional density diagram.
        dropPm : :class:`bool`
            Whether to exclude the (almost) non-existent element Promethium from the REE
            list.
        scatter_kw : :class:`dict`
            Keyword parameters to be passed to the scatter plotting function.
        line_kw : :class:`dict`
            Keyword parameters to be passed to the line plotting function.
        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the REE plot is added.

        """
        obj = to_frame(self._obj)
        ree = [i for i in geochem.ind.REE(dropPm=dropPm) if i in obj.columns]

        ax = spider.REE_v_radii(
            obj.reindex(columns=ree).astype(float).values,
            index=index,
            ree=ree,
            mode=mode,
            ax=ax,
            scatter_kw=scatter_kw,
            line_kw=line_kw,
            **kwargs,
        )
        ax.set_ylabel(r"$\mathrm{X / X_{Reference}}$")
        return ax

    def scatter(self, components: list = None, ax=None, axlabels=True, **kwargs):
        r"""
        Convenience method for scatter plots using the pyroplot API. See
        further parameters for `matplotlib.pyplot.scatter` function below.

        Parameters
        ----------
        components : :class:`list`, :code:`None`
            Elements or compositional components to plot.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        axlabels : :class:`bool`, :code:`True`
            Whether to add x-y axis labels.
        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the scatterplot is added.

        """
        obj = to_frame(self._obj)
        components = _check_components(obj, components=components)

        projection = [None, "ternary"][len(components) == 3]
        ax = init_axes(ax=ax, projection=projection, **kwargs)
        size = obj.index.size
        kw = process_color(size=size, **kwargs)
        with warnings.catch_warnings():
            # ternary transform where points add to zero will give an unnecessary
            # warning; here we supress it
            warnings.filterwarnings(
                "ignore", message="invalid value encountered in divide"
            )
            ax.scatter(*obj.reindex(columns=components).values.T, **scatterkwargs(kw))

        if axlabels:
            label_axes(ax, labels=components)

        ax.tick_params("both")
        # ax.grid()
        # ax.set_aspect("equal")
        return ax

    def spider(
        self,
        components: list = None,
        indexes: list = None,
        ax=None,
        mode="plot",
        index_order=None,
        autoscale=True,
        scatter_kw={},
        line_kw={},
        **kwargs,
    ):
        r"""
        Method for spider plots. Convenience access function to
        :func:`~pyrolite.plot.spider.spider` (see `Other Parameters`, below), where
        further parameters for relevant `matplotlib` functions are also listed.

        Parameters
        ----------
        components : :class:`list`, `None`
            Elements or compositional components to plot.
        indexes :  :class:`list`, `None`
            Elements or compositional components to plot.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        index_order
            Function to order spider plot indexes (e.g. by incompatibility).
        autoscale : :class:`bool`
            Whether to autoscale the y-axis limits for standard spider plots.
        mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
            Mode for plot. Plot will produce a line-scatter diagram. Fill will return
            a filled range. Density will return a conditional density diagram.
        scatter_kw : :class:`dict`
            Keyword parameters to be passed to the scatter plotting function.
        line_kw : :class:`dict`
            Keyword parameters to be passed to the line plotting function.
        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the spider diagram is plotted.

        Todo
        ----
            * Add 'compositional data' filter for default components if None is given

        """
        obj = to_frame(self._obj)

        if components is None:  # default to plotting elemental data
            components = [
                el for el in obj.columns if el in geochem.ind.common_elements()
            ]

        assert len(components) != 0

        if index_order is not None:
            if isinstance(index_order, str):
                try:
                    index_order = geochem.ind.ordering[index_order]
                except KeyError:
                    msg = (
                        "Ordering not applied, as parameter '{}' not recognized."
                        " Select from: {}"
                    ).format(index_order, ", ".join(list(geochem.ind.ordering.keys())))
                    logger.warning(msg)
                components = index_order(components)
            else:
                components = index_order(components)

        ax = init_axes(ax=ax, **kwargs)

        if hasattr(ax, "_pyrolite_components"):
            # TODO: handle spider diagrams which have specified components
            pass

        ax = spider.spider(
            obj.reindex(columns=components).astype(float).values,
            indexes=indexes,
            ax=ax,
            mode=mode,
            autoscale=autoscale,
            scatter_kw=scatter_kw,
            line_kw=line_kw,
            **kwargs,
        )
        ax._pyrolite_components = components
        ax.set_xticklabels(components, rotation=60)
        return ax

    def stem(
        self,
        components: list = None,
        ax=None,
        orientation="horizontal",
        axlabels=True,
        **kwargs,
    ):
        r"""
        Method for creating stem plots. Convenience access function to
        :func:`~pyrolite.plot.stem.stem` (see `Other Parameters`, below), where
        further parameters for relevant `matplotlib` functions are also listed.

        Parameters
        ----------
        components : :class:`list`, :code:`None`
            Elements or compositional components to plot.
        ax : :class:`matplotlib.axes.Axes`, :code:`None`
            The subplot to draw on.
        orientation : :class:`str`
            Orientation of the plot (horizontal or vertical).
        axlabels : :class:`bool`, True
            Whether to add x-y axis labels.
        {otherparams}

        Returns
        -------
        :class:`matplotlib.axes.Axes`
            Axes on which the stem diagram is plotted.
        """
        obj = to_frame(self._obj)
        components = _check_components(obj, components=components, valid_sizes=[2])

        ax = stem.stem(
            *obj.reindex(columns=components).values.T,
            ax=ax,
            orientation=orientation,
            **process_color(**kwargs),
        )

        if axlabels:
            if "h" not in orientation.lower():
                components = components[::-1]
            label_axes(ax, labels=components)

        return ax


pyroplot = pyroplot_matplotlib


# note that only some of these methods will be valid for series
pd.api.extensions.register_series_accessor("pyroplot")(pyroplot)
pd.api.extensions.register_dataframe_accessor("pyroplot")(pyroplot)


# ideally we would i) check for the same params and ii) aggregate all others across
# inherited or chained functions. This simply imports the params from another docstring
_add_additional_parameters = True

pyroplot.density.__doc__ = pyroplot.density.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.density,
            density.density,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)

pyroplot.parallel.__doc__ = pyroplot.parallel.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.parallel,
            parallel.parallel,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)


pyroplot.REE.__doc__ = pyroplot.REE.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.REE,
            spider.REE_v_radii,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)


pyroplot.scatter.__doc__ = pyroplot.scatter.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.scatter,
            plt.scatter,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)

pyroplot.plot.__doc__ = pyroplot.plot.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.plot,
            plt.plot,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)

pyroplot.spider.__doc__ = pyroplot.spider.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.spider,
            spider.spider,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)


pyroplot.stem.__doc__ = pyroplot.stem.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.stem,
            stem.stem,
            header="Other Parameters",
            indent=8,
            subsections=True,
        ),
    ][_add_additional_parameters]
)

pyroplot.heatscatter.__doc__ = pyroplot.heatscatter.__doc__.format(
    otherparams=[
        "",
        get_additional_params(
            pyroplot.scatter, header="Other Parameters", indent=8, subsections=True
        ),
    ][_add_additional_parameters]
)

1	"""
2	Submodule with various plotting and visualisation functions.
3	"""
4
5	import warnings	12✔
6
7	import matplotlib	12✔
8	import matplotlib.pyplot as plt	12✔
9	import mpltern	12✔
10	import numpy as np	12✔
11	import pandas as pd	12✔
12
13	warnings.filterwarnings("ignore", "Unknown section")	12✔
14
15	from .. import geochem	12✔
16	from ..comp.codata import ILR, close	12✔
17	from ..util.distributions import get_scaler, sample_kde	12✔
18	from ..util.log import Handle	12✔
19	from ..util.meta import get_additional_params, subkwargs	12✔
20	from ..util.pd import to_frame, _check_components	12✔
21	from ..util.plot.axes import init_axes, label_axes	12✔
22	from ..util.plot.helpers import plot_cooccurence	12✔
23	from ..util.plot.style import _export_nonRCstyles, linekwargs, scatterkwargs	12✔
24	from . import density, parallel, spider, stem	12✔
25	from .color import process_color	12✔
26
27	logger = Handle(__name__)	12✔
28
29	# pyroplot added to __all__ for docs
30	__all__ = ["density", "spider", "pyroplot"]	12✔
31
32
33	class pyroplot_matplotlib(object):	12✔
34	def __init__(self, obj):	12✔
35	"""
36	Custom dataframe accessor for pyrolite plotting.
37
38	Notes
39	-----
40	This accessor enables the coexistence of array-based plotting functions and
41	methods for pandas objects. This enables some separation of concerns.
42	"""
43	self._validate(obj)	12✔
44	self._obj = obj	12✔
45
46	# refresh custom styling on creation?
47	_export_nonRCstyles()	12✔
48
49	@staticmethod	12✔
50	def _validate(obj):	12✔
51	pass	12✔
52
53	def cooccurence(self, ax=None, normalize=True, log=False, colorbar=False, **kwargs):	12✔
54	"""
55	Plot the co-occurence frequency matrix for a given input.
56
57	Parameters
58	----------
59	ax : :class:`matplotlib.axes.Axes`, :code:`None`
60	The subplot to draw on.
61	normalize : :class:`bool`
62	Whether to normalize the cooccurence to compare disparate variables.
63	log : :class:`bool`
64	Whether to take the log of the cooccurence.
65	colorbar : :class:`bool`
66	Whether to append a colorbar.
67
68	Returns
69	-------
70	:class:`matplotlib.axes.Axes`
71	Axes on which the cooccurence plot is added.
72
73	"""
74	obj = to_frame(self._obj)	12✔
75	ax = plot_cooccurence(	12✔
76	obj.values, ax=ax, normalize=normalize, log=log, colorbar=colorbar, **kwargs
77	)
78	ax.set_xticklabels(obj.columns, minor=False, rotation=90)	12✔
79	ax.set_yticklabels(obj.columns, minor=False)	12✔
80	return ax	12✔
81
82	def density(self, components: list = None, ax=None, axlabels=True, **kwargs):	12✔
83	r"""
84	Method for plotting histograms (mode='hist2d'\|'hexbin') or kernel density
85	esitimates from point data. Convenience access function to
86	:func:`~pyrolite.plot.density.density` (see `Other Parameters`, below), where
87	further parameters for relevant `matplotlib` functions are also listed.
88
89	Parameters
90	----------
91	components : :class:`list`, :code:`None`
92	Elements or compositional components to plot.
93	ax : :class:`matplotlib.axes.Axes`, :code:`None`
94	The subplot to draw on.
95	axlabels : :class:`bool`, True
96	Whether to add x-y axis labels.
97
98	{otherparams}
99
100	Returns
101	-------
102	:class:`matplotlib.axes.Axes`
103	Axes on which the density diagram is plotted.
104
105	"""
106	obj = to_frame(self._obj)	12✔
107	components = _check_components(obj, components=components)	12✔
108
109	ax = density.density(	12✔
110	obj.reindex(columns=components).astype(float).values, ax=ax, **kwargs
111	)
112	if axlabels:	12✔
113	label_axes(ax, labels=components)	12✔
114
115	return ax	12✔
116
117	def heatscatter(	12✔
118	self,
119	components: list = None,
120	ax=None,
121	axlabels=True,
122	logx=False,
123	logy=False,
124	**kwargs,
125	):
126	r"""
127	Heatmapped scatter plots using the pyroplot API. See further parameters
128	for `matplotlib.pyplot.scatter` function below.
129
130	Parameters
131	----------
132	components : :class:`list`, :code:`None`
133	Elements or compositional components to plot.
134	ax : :class:`matplotlib.axes.Axes`, :code:`None`
135	The subplot to draw on.
136	axlabels : :class:`bool`, :code:`True`
137	Whether to add x-y axis labels.
138	logx : :class:`bool`, `False`
139	Whether to log-transform x values before the KDE for bivariate plots.
140	logy : :class:`bool`, `False`
141	Whether to log-transform y values before the KDE for bivariate plots.
142
143	{otherparams}
144
145	Returns
146	-------
147	:class:`matplotlib.axes.Axes`
148	Axes on which the heatmapped scatterplot is added.
149
150	"""
151	obj = to_frame(self._obj)	12✔
152	components = _check_components(obj, components=components)	12✔
153	data, samples = (	12✔
154	obj.reindex(columns=components).values,
155	obj.reindex(columns=components).values,
156	)
157	kdetfm = [ # log transforms	12✔
158	get_scaler([None, np.log][logx], [None, np.log][logy]),
159	lambda x: ILR(close(x)),
160	][len(components) == 3]
161	zi = sample_kde(	12✔
162	data, samples, transform=kdetfm, **subkwargs(kwargs, sample_kde)
163	)
164	kwargs.update({"c": zi})	12✔
165	ax = obj.reindex(columns=components).pyroplot.scatter(	12✔
166	ax=ax, axlabels=axlabels, **kwargs
167	)
168	return ax	12✔
169
170	def parallel(	12✔
171	self,
172	components=None,
173	rescale=False,
174	legend=False,
175	ax=None,
176	**kwargs,
177	):
178	"""
179	Create a :func:`pyrolite.plot.parallel.parallel`. coordinate plot from
180	the columns of the :class:`~pandas.DataFrame`.
181
182	Parameters
183	----------
184	components : :class:`list`, :code:`None`
185	Components to use as axes for the plot.
186	rescale : :class:`bool`
187	Whether to rescale values to [-1, 1].
188	legend : :class:`bool`, :code:`False`
189	Whether to include or suppress the legend.
190	ax : :class:`matplotlib.axes.Axes`, :code:`None`
191	The subplot to draw on.
192	{otherparams}
193
194	Returns
195	-------
196	:class:`matplotlib.axes.Axes`
197	Axes on which the parallel coordinates plot is added.
198
199	Todo
200	----
201	* Adapt figure size based on number of columns.
202
203	"""
204
205	obj = to_frame(self._obj)	12✔
206	ax = parallel.parallel(	12✔
207	obj,
208	components=components,
209	rescale=rescale,
210	legend=legend,
211	ax=ax,
212	**kwargs,
213	)
214	return ax	12✔
215
216	def plot(self, components: list = None, ax=None, axlabels=True, **kwargs):	12✔
217	r"""
218	Convenience method for line plots using the pyroplot API. See
219	further parameters for `matplotlib.pyplot.scatter` function below.
220
221	Parameters
222	----------
223	components : :class:`list`, :code:`None`
224	Elements or compositional components to plot.
225	ax : :class:`matplotlib.axes.Axes`, :code:`None`
226	The subplot to draw on.
227	axlabels : :class:`bool`, :code:`True`
228	Whether to add x-y axis labels.
229	{otherparams}
230
231	Returns
232	-------
233	:class:`matplotlib.axes.Axes`
234	Axes on which the plot is added.
235
236	"""
237	obj = to_frame(self._obj)	×
238	components = _check_components(obj, components=components)	×
239	projection = [None, "ternary"][len(components) == 3]	×
240	ax = init_axes(ax=ax, projection=projection, **kwargs)	×
241	kw = linekwargs(kwargs)	×
242	ax.plot(obj.reindex(columns=components).values.T, *kw)	×
243	# if color is multi, could update line colors here
244	if axlabels:	×
245	label_axes(ax, labels=components)	×
246
247	ax.tick_params("both")	×
248	# ax.grid()
249	# ax.set_aspect("equal")
250	return ax	×
251
252	def REE(	12✔
253	self,
254	index="elements",
255	ax=None,
256	mode="plot",
257	dropPm=True,
258	scatter_kw={},
259	line_kw={},
260	**kwargs,
261	):
262	"""Pass the pandas object to :func:`pyrolite.plot.spider.REE_v_radii`.
263
264	Parameters
265	----------
266	ax : :class:`matplotlib.axes.Axes`, :code:`None`
267	The subplot to draw on.
268	index : :class:`str`
269	Whether to plot radii ('radii') on the principal x-axis, or elements
270	('elements').
271	mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
272	Mode for plot. Plot will produce a line-scatter diagram. Fill will return
273	a filled range. Density will return a conditional density diagram.
274	dropPm : :class:`bool`
275	Whether to exclude the (almost) non-existent element Promethium from the REE
276	list.
277	scatter_kw : :class:`dict`
278	Keyword parameters to be passed to the scatter plotting function.
279	line_kw : :class:`dict`
280	Keyword parameters to be passed to the line plotting function.
281	{otherparams}
282
283	Returns
284	-------
285	:class:`matplotlib.axes.Axes`
286	Axes on which the REE plot is added.
287
288	"""
289	obj = to_frame(self._obj)	12✔
290	ree = [i for i in geochem.ind.REE(dropPm=dropPm) if i in obj.columns]	12✔
291
292	ax = spider.REE_v_radii(	12✔
293	obj.reindex(columns=ree).astype(float).values,
294	index=index,
295	ree=ree,
296	mode=mode,
297	ax=ax,
298	scatter_kw=scatter_kw,
299	line_kw=line_kw,
300	**kwargs,
301	)
302	ax.set_ylabel(r"$\mathrm{X / X_{Reference}}$")	12✔
303	return ax	12✔
304
305	def scatter(self, components: list = None, ax=None, axlabels=True, **kwargs):	12✔
306	r"""
307	Convenience method for scatter plots using the pyroplot API. See
308	further parameters for `matplotlib.pyplot.scatter` function below.
309
310	Parameters
311	----------
312	components : :class:`list`, :code:`None`
313	Elements or compositional components to plot.
314	ax : :class:`matplotlib.axes.Axes`, :code:`None`
315	The subplot to draw on.
316	axlabels : :class:`bool`, :code:`True`
317	Whether to add x-y axis labels.
318	{otherparams}
319
320	Returns
321	-------
322	:class:`matplotlib.axes.Axes`
323	Axes on which the scatterplot is added.
324
325	"""
326	obj = to_frame(self._obj)	12✔
327	components = _check_components(obj, components=components)	12✔
328
329	projection = [None, "ternary"][len(components) == 3]	12✔
330	ax = init_axes(ax=ax, projection=projection, **kwargs)	12✔
331	size = obj.index.size	12✔
332	kw = process_color(size=size, **kwargs)	12✔
333	with warnings.catch_warnings():	12✔
334	# ternary transform where points add to zero will give an unnecessary
335	# warning; here we supress it
336	warnings.filterwarnings(	12✔
337	"ignore", message="invalid value encountered in divide"
338	)
339	ax.scatter(obj.reindex(columns=components).values.T, *scatterkwargs(kw))	12✔
340
341	if axlabels:	12✔
342	label_axes(ax, labels=components)	12✔
343
344	ax.tick_params("both")	12✔
345	# ax.grid()
346	# ax.set_aspect("equal")
347	return ax	12✔
348
349	def spider(	12✔
350	self,
351	components: list = None,
352	indexes: list = None,
353	ax=None,
354	mode="plot",
355	index_order=None,
356	autoscale=True,
357	scatter_kw={},
358	line_kw={},
359	**kwargs,
360	):
361	r"""
362	Method for spider plots. Convenience access function to
363	:func:`~pyrolite.plot.spider.spider` (see `Other Parameters`, below), where
364	further parameters for relevant `matplotlib` functions are also listed.
365
366	Parameters
367	----------
368	components : :class:`list`, `None`
369	Elements or compositional components to plot.
370	indexes : :class:`list`, `None`
371	Elements or compositional components to plot.
372	ax : :class:`matplotlib.axes.Axes`, :code:`None`
373	The subplot to draw on.
374	index_order
375	Function to order spider plot indexes (e.g. by incompatibility).
376	autoscale : :class:`bool`
377	Whether to autoscale the y-axis limits for standard spider plots.
378	mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
379	Mode for plot. Plot will produce a line-scatter diagram. Fill will return
380	a filled range. Density will return a conditional density diagram.
381	scatter_kw : :class:`dict`
382	Keyword parameters to be passed to the scatter plotting function.
383	line_kw : :class:`dict`
384	Keyword parameters to be passed to the line plotting function.
385	{otherparams}
386
387	Returns
388	-------
389	:class:`matplotlib.axes.Axes`
390	Axes on which the spider diagram is plotted.
391
392	Todo
393	----
394	* Add 'compositional data' filter for default components if None is given
395
396	"""
397	obj = to_frame(self._obj)	12✔
398
399	if components is None: # default to plotting elemental data	12✔
400	components = [	12✔
401	el for el in obj.columns if el in geochem.ind.common_elements()
402	]
403
404	assert len(components) != 0	12✔
405
406	if index_order is not None:	12✔
407	if isinstance(index_order, str):	×
408	try:	×
409	index_order = geochem.ind.ordering[index_order]	×
410	except KeyError:	×
411	msg = (	×
412	"Ordering not applied, as parameter '{}' not recognized."
413	" Select from: {}"
414	).format(index_order, ", ".join(list(geochem.ind.ordering.keys())))
415	logger.warning(msg)	×
416	components = index_order(components)	×
417	else:
418	components = index_order(components)	×
419
420	ax = init_axes(ax=ax, **kwargs)	12✔
421
422	if hasattr(ax, "_pyrolite_components"):	12✔
423	# TODO: handle spider diagrams which have specified components
424	pass
425
426	ax = spider.spider(	12✔
427	obj.reindex(columns=components).astype(float).values,
428	indexes=indexes,
429	ax=ax,
430	mode=mode,
431	autoscale=autoscale,
432	scatter_kw=scatter_kw,
433	line_kw=line_kw,
434	**kwargs,
435	)
436	ax._pyrolite_components = components	12✔
437	ax.set_xticklabels(components, rotation=60)	12✔
438	return ax	12✔
439
440	def stem(	12✔
441	self,
442	components: list = None,
443	ax=None,
444	orientation="horizontal",
445	axlabels=True,
446	**kwargs,
447	):
448	r"""
449	Method for creating stem plots. Convenience access function to
450	:func:`~pyrolite.plot.stem.stem` (see `Other Parameters`, below), where
451	further parameters for relevant `matplotlib` functions are also listed.
452
453	Parameters
454	----------
455	components : :class:`list`, :code:`None`
456	Elements or compositional components to plot.
457	ax : :class:`matplotlib.axes.Axes`, :code:`None`
458	The subplot to draw on.
459	orientation : :class:`str`
460	Orientation of the plot (horizontal or vertical).
461	axlabels : :class:`bool`, True
462	Whether to add x-y axis labels.
463	{otherparams}
464
465	Returns
466	-------
467	:class:`matplotlib.axes.Axes`
468	Axes on which the stem diagram is plotted.
469	"""
470	obj = to_frame(self._obj)	12✔
471	components = _check_components(obj, components=components, valid_sizes=[2])	12✔
472
473	ax = stem.stem(	12✔
474	*obj.reindex(columns=components).values.T,
475	ax=ax,
476	orientation=orientation,
477	process_color(kwargs),
478	)
479
480	if axlabels:	12✔
481	if "h" not in orientation.lower():	12✔
482	components = components[::-1]	12✔
483	label_axes(ax, labels=components)	12✔
484
485	return ax	12✔
486
487
488	pyroplot = pyroplot_matplotlib	12✔
489
490
491	# note that only some of these methods will be valid for series
492	pd.api.extensions.register_series_accessor("pyroplot")(pyroplot)	12✔
493	pd.api.extensions.register_dataframe_accessor("pyroplot")(pyroplot)	12✔
494
495
496	# ideally we would i) check for the same params and ii) aggregate all others across
497	# inherited or chained functions. This simply imports the params from another docstring
498	_add_additional_parameters = True	12✔
499
500	pyroplot.density.__doc__ = pyroplot.density.__doc__.format(	12✔
501	otherparams=[
502	"",
503	get_additional_params(
504	pyroplot.density,
505	density.density,
506	header="Other Parameters",
507	indent=8,
508	subsections=True,
509	),
510	][_add_additional_parameters]
511	)
512
513	pyroplot.parallel.__doc__ = pyroplot.parallel.__doc__.format(	12✔
514	otherparams=[
515	"",
516	get_additional_params(
517	pyroplot.parallel,
518	parallel.parallel,
519	header="Other Parameters",
520	indent=8,
521	subsections=True,
522	),
523	][_add_additional_parameters]
524	)
525
526
527	pyroplot.REE.__doc__ = pyroplot.REE.__doc__.format(	12✔
528	otherparams=[
529	"",
530	get_additional_params(
531	pyroplot.REE,
532	spider.REE_v_radii,
533	header="Other Parameters",
534	indent=8,
535	subsections=True,
536	),
537	][_add_additional_parameters]
538	)
539
540
541	pyroplot.scatter.__doc__ = pyroplot.scatter.__doc__.format(	12✔
542	otherparams=[
543	"",
544	get_additional_params(
545	pyroplot.scatter,
546	plt.scatter,
547	header="Other Parameters",
548	indent=8,
549	subsections=True,
550	),
551	][_add_additional_parameters]
552	)
553
554	pyroplot.plot.__doc__ = pyroplot.plot.__doc__.format(	12✔
555	otherparams=[
556	"",
557	get_additional_params(
558	pyroplot.plot,
559	plt.plot,
560	header="Other Parameters",
561	indent=8,
562	subsections=True,
563	),
564	][_add_additional_parameters]
565	)
566
567	pyroplot.spider.__doc__ = pyroplot.spider.__doc__.format(	12✔
568	otherparams=[
569	"",
570	get_additional_params(
571	pyroplot.spider,
572	spider.spider,
573	header="Other Parameters",
574	indent=8,
575	subsections=True,
576	),
577	][_add_additional_parameters]
578	)
579
580
581	pyroplot.stem.__doc__ = pyroplot.stem.__doc__.format(	12✔
582	otherparams=[
583	"",
584	get_additional_params(
585	pyroplot.stem,
586	stem.stem,
587	header="Other Parameters",
588	indent=8,
589	subsections=True,
590	),
591	][_add_additional_parameters]
592	)
593
594	pyroplot.heatscatter.__doc__ = pyroplot.heatscatter.__doc__.format(	12✔
595	otherparams=[
596	"",
597	get_additional_params(
598	pyroplot.scatter, header="Other Parameters", indent=8, subsections=True
599	),
600	][_add_additional_parameters]
601	)

morganjwilliams / pyrolite / 11836306515

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