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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
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"]


def _check_components(obj, components=None, check_size=True, valid_sizes=[2, 3]):
    """
    Check that the components provided within a dataframe are consistent with the
    form of plot being used.

    Parameters
    ----------
    obj : :class:`pandas.DataFrame`
        Object to check.
    components : :class:`list`
        List of components, optionally specified.
    check_size : :class:`bool`
        Whether to verify the size of the column index.
    valid_sizes : :class:`list`
        Component list lengths which are valid for the plot type.

    Returns
    -------
    :class:`list`
        Components for the plot.
    """
    try:
        if check_size and (obj.columns.size not in valid_sizes):
            assert len(components) in valid_sizes

        if components is None:
            components = obj.columns.values
    except:
        msg = "Suggest components or provide a slice of the dataframe."
        raise AssertionError(msg)
    return components


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


# 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	import warnings	12✔
5
6	import matplotlib	12✔
7	import matplotlib.pyplot as plt	12✔
8	import mpltern	12✔
9	import numpy as np	12✔
10	import pandas as pd	12✔
11
12	warnings.filterwarnings("ignore", "Unknown section")	12✔
13
14	from .. import geochem	12✔
15	from ..comp.codata import ILR, close	12✔
16	from ..util.distributions import get_scaler, sample_kde	12✔
17	from ..util.log import Handle	12✔
18	from ..util.meta import get_additional_params, subkwargs	12✔
19	from ..util.pd import to_frame	12✔
20	from ..util.plot.axes import init_axes, label_axes	12✔
21	from ..util.plot.helpers import plot_cooccurence	12✔
22	from ..util.plot.style import _export_nonRCstyles, linekwargs, scatterkwargs	12✔
23	from . import density, parallel, spider, stem	12✔
24	from .color import process_color	12✔
25
26	logger = Handle(__name__)	12✔
27
28	# pyroplot added to __all__ for docs
29	__all__ = ["density", "spider", "pyroplot"]	12✔
30
31
32	def _check_components(obj, components=None, check_size=True, valid_sizes=[2, 3]):	12✔
33	"""
34	Check that the components provided within a dataframe are consistent with the
35	form of plot being used.
36
37	Parameters
38	----------
39	obj : :class:`pandas.DataFrame`
40	Object to check.
41	components : :class:`list`
42	List of components, optionally specified.
43	check_size : :class:`bool`
44	Whether to verify the size of the column index.
45	valid_sizes : :class:`list`
46	Component list lengths which are valid for the plot type.
47
48	Returns
49	-------
50	:class:`list`
51	Components for the plot.
52	"""
53	try:	12✔
54	if check_size and (obj.columns.size not in valid_sizes):	12✔
55	assert len(components) in valid_sizes	12✔
56
57	if components is None:	12✔
58	components = obj.columns.values	12✔
59	except:	12✔
60	msg = "Suggest components or provide a slice of the dataframe."	12✔
61	raise AssertionError(msg)	12✔
62	return components	12✔
63
64
65	# note that only some of these methods will be valid for series
66	@pd.api.extensions.register_series_accessor("pyroplot")	12✔
67	@pd.api.extensions.register_dataframe_accessor("pyroplot")	12✔
68	class pyroplot(object):	12✔
69	def __init__(self, obj):	12✔
70	"""
71	Custom dataframe accessor for pyrolite plotting.
72
73	Notes
74	-----
75	This accessor enables the coexistence of array-based plotting functions and
76	methods for pandas objects. This enables some separation of concerns.
77	"""
78	self._validate(obj)	12✔
79	self._obj = obj	12✔
80
81	# refresh custom styling on creation?
82	_export_nonRCstyles()	12✔
83
84	@staticmethod	12✔
85	def _validate(obj):	12✔
86	pass	12✔
87
88	def cooccurence(self, ax=None, normalize=True, log=False, colorbar=False, **kwargs):	12✔
89	"""
90	Plot the co-occurence frequency matrix for a given input.
91
92	Parameters
93	----------
94	ax : :class:`matplotlib.axes.Axes`, :code:`None`
95	The subplot to draw on.
96	normalize : :class:`bool`
97	Whether to normalize the cooccurence to compare disparate variables.
98	log : :class:`bool`
99	Whether to take the log of the cooccurence.
100	colorbar : :class:`bool`
101	Whether to append a colorbar.
102
103	Returns
104	-------
105	:class:`matplotlib.axes.Axes`
106	Axes on which the cooccurence plot is added.
107
108	"""
109	obj = to_frame(self._obj)	12✔
110	ax = plot_cooccurence(	12✔
111	obj.values, ax=ax, normalize=normalize, log=log, colorbar=colorbar, **kwargs
112	)
113	ax.set_xticklabels(obj.columns, minor=False, rotation=90)	12✔
114	ax.set_yticklabels(obj.columns, minor=False)	12✔
115	return ax	12✔
116
117	def density(self, components: list = None, ax=None, axlabels=True, **kwargs):	12✔
118	r"""
119	Method for plotting histograms (mode='hist2d'\|'hexbin') or kernel density
120	esitimates from point data. Convenience access function to
121	:func:`~pyrolite.plot.density.density` (see `Other Parameters`, below), where
122	further parameters for relevant `matplotlib` functions are also listed.
123
124	Parameters
125	----------
126	components : :class:`list`, :code:`None`
127	Elements or compositional components to plot.
128	ax : :class:`matplotlib.axes.Axes`, :code:`None`
129	The subplot to draw on.
130	axlabels : :class:`bool`, True
131	Whether to add x-y axis labels.
132
133	{otherparams}
134
135	Returns
136	-------
137	:class:`matplotlib.axes.Axes`
138	Axes on which the density diagram is plotted.
139
140	"""
141	obj = to_frame(self._obj)	12✔
142	components = _check_components(obj, components=components)	12✔
143
144	ax = density.density(	12✔
145	obj.reindex(columns=components).astype(float).values, ax=ax, **kwargs
146	)
147	if axlabels:	12✔
148	label_axes(ax, labels=components)	12✔
149
150	return ax	12✔
151
152	def heatscatter(	12✔
153	self,
154	components: list = None,
155	ax=None,
156	axlabels=True,
157	logx=False,
158	logy=False,
159	**kwargs,
160	):
161	r"""
162	Heatmapped scatter plots using the pyroplot API. See further parameters
163	for `matplotlib.pyplot.scatter` function below.
164
165	Parameters
166	----------
167	components : :class:`list`, :code:`None`
168	Elements or compositional components to plot.
169	ax : :class:`matplotlib.axes.Axes`, :code:`None`
170	The subplot to draw on.
171	axlabels : :class:`bool`, :code:`True`
172	Whether to add x-y axis labels.
173	logx : :class:`bool`, `False`
174	Whether to log-transform x values before the KDE for bivariate plots.
175	logy : :class:`bool`, `False`
176	Whether to log-transform y values before the KDE for bivariate plots.
177
178	{otherparams}
179
180	Returns
181	-------
182	:class:`matplotlib.axes.Axes`
183	Axes on which the heatmapped scatterplot is added.
184
185	"""
186	obj = to_frame(self._obj)	12✔
187	components = _check_components(obj, components=components)	12✔
188	data, samples = (	12✔
189	obj.reindex(columns=components).values,
190	obj.reindex(columns=components).values,
191	)
192	kdetfm = [ # log transforms	12✔
193	get_scaler([None, np.log][logx], [None, np.log][logy]),
194	lambda x: ILR(close(x)),
195	][len(components) == 3]
196	zi = sample_kde(	12✔
197	data, samples, transform=kdetfm, **subkwargs(kwargs, sample_kde)
198	)
199	kwargs.update({"c": zi})	12✔
200	ax = obj.reindex(columns=components).pyroplot.scatter(	12✔
201	ax=ax, axlabels=axlabels, **kwargs
202	)
203	return ax	12✔
204
205	def parallel(	12✔
206	self,
207	components=None,
208	rescale=False,
209	legend=False,
210	ax=None,
211	**kwargs,
212	):
213	"""
214	Create a :func:`pyrolite.plot.parallel.parallel`. coordinate plot from
215	the columns of the :class:`~pandas.DataFrame`.
216
217	Parameters
218	----------
219	components : :class:`list`, :code:`None`
220	Components to use as axes for the plot.
221	rescale : :class:`bool`
222	Whether to rescale values to [-1, 1].
223	legend : :class:`bool`, :code:`False`
224	Whether to include or suppress the legend.
225	ax : :class:`matplotlib.axes.Axes`, :code:`None`
226	The subplot to draw on.
227	{otherparams}
228
229	Returns
230	-------
231	:class:`matplotlib.axes.Axes`
232	Axes on which the parallel coordinates plot is added.
233
234	Todo
235	----
236	* Adapt figure size based on number of columns.
237
238	"""
239
240	obj = to_frame(self._obj)	12✔
241	ax = parallel.parallel(	12✔
242	obj,
243	components=components,
244	rescale=rescale,
245	legend=legend,
246	ax=ax,
247	**kwargs,
248	)
249	return ax	12✔
250
251	def plot(self, components: list = None, ax=None, axlabels=True, **kwargs):	12✔
252	r"""
253	Convenience method for line plots using the pyroplot API. See
254	further parameters for `matplotlib.pyplot.scatter` function below.
255
256	Parameters
257	----------
258	components : :class:`list`, :code:`None`
259	Elements or compositional components to plot.
260	ax : :class:`matplotlib.axes.Axes`, :code:`None`
261	The subplot to draw on.
262	axlabels : :class:`bool`, :code:`True`
263	Whether to add x-y axis labels.
264	{otherparams}
265
266	Returns
267	-------
268	:class:`matplotlib.axes.Axes`
269	Axes on which the plot is added.
270
271	"""
272	obj = to_frame(self._obj)	×
273	components = _check_components(obj, components=components)	×
UNCOV 274	projection = [None, "ternary"][len(components) == 3]	×
275	ax = init_axes(ax=ax, projection=projection, **kwargs)	×
276	kw = linekwargs(kwargs)	×
NEW 277	ax.plot(obj.reindex(columns=components).values.T, *kw)	×
278	# if color is multi, could update line colors here
UNCOV 279	if axlabels:	×
UNCOV 280	label_axes(ax, labels=components)	×
281
UNCOV 282	ax.tick_params("both")	×
283	# ax.grid()
284	# ax.set_aspect("equal")
UNCOV 285	return ax	×
286
287	def REE(	12✔
288	self,
289	index="elements",
290	ax=None,
291	mode="plot",
292	dropPm=True,
293	scatter_kw={},
294	line_kw={},
295	**kwargs,
296	):
297	"""Pass the pandas object to :func:`pyrolite.plot.spider.REE_v_radii`.
298
299	Parameters
300	----------
301	ax : :class:`matplotlib.axes.Axes`, :code:`None`
302	The subplot to draw on.
303	index : :class:`str`
304	Whether to plot radii ('radii') on the principal x-axis, or elements
305	('elements').
306	mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
307	Mode for plot. Plot will produce a line-scatter diagram. Fill will return
308	a filled range. Density will return a conditional density diagram.
309	dropPm : :class:`bool`
310	Whether to exclude the (almost) non-existent element Promethium from the REE
311	list.
312	scatter_kw : :class:`dict`
313	Keyword parameters to be passed to the scatter plotting function.
314	line_kw : :class:`dict`
315	Keyword parameters to be passed to the line plotting function.
316	{otherparams}
317
318	Returns
319	-------
320	:class:`matplotlib.axes.Axes`
321	Axes on which the REE plot is added.
322
323	"""
324	obj = to_frame(self._obj)	12✔
325	ree = [i for i in geochem.ind.REE(dropPm=dropPm) if i in obj.columns]	12✔
326
327	ax = spider.REE_v_radii(	12✔
328	obj.reindex(columns=ree).astype(float).values,
329	index=index,
330	ree=ree,
331	mode=mode,
332	ax=ax,
333	scatter_kw=scatter_kw,
334	line_kw=line_kw,
335	**kwargs,
336	)
337	ax.set_ylabel(r"$\mathrm{X / X_{Reference}}$")	12✔
338	return ax	12✔
339
340	def scatter(self, components: list = None, ax=None, axlabels=True, **kwargs):	12✔
341	r"""
342	Convenience method for scatter plots using the pyroplot API. See
343	further parameters for `matplotlib.pyplot.scatter` function below.
344
345	Parameters
346	----------
347	components : :class:`list`, :code:`None`
348	Elements or compositional components to plot.
349	ax : :class:`matplotlib.axes.Axes`, :code:`None`
350	The subplot to draw on.
351	axlabels : :class:`bool`, :code:`True`
352	Whether to add x-y axis labels.
353	{otherparams}
354
355	Returns
356	-------
357	:class:`matplotlib.axes.Axes`
358	Axes on which the scatterplot is added.
359
360	"""
361	obj = to_frame(self._obj)	12✔
362	components = _check_components(obj, components=components)	12✔
363
364	projection = [None, "ternary"][len(components) == 3]	12✔
365	ax = init_axes(ax=ax, projection=projection, **kwargs)	12✔
366	size = obj.index.size	12✔
367	kw = process_color(size=size, **kwargs)	12✔
368	with warnings.catch_warnings():	12✔
369	# ternary transform where points add to zero will give an unnecessary
370	# warning; here we supress it
371	warnings.filterwarnings(	12✔
372	"ignore", message="invalid value encountered in divide"
373	)
374	ax.scatter(obj.reindex(columns=components).values.T, *scatterkwargs(kw))	12✔
375
376	if axlabels:	12✔
377	label_axes(ax, labels=components)	12✔
378
379	ax.tick_params("both")	12✔
380	# ax.grid()
381	# ax.set_aspect("equal")
382	return ax	12✔
383
384	def spider(	12✔
385	self,
386	components: list = None,
387	indexes: list = None,
388	ax=None,
389	mode="plot",
390	index_order=None,
391	autoscale=True,
392	scatter_kw={},
393	line_kw={},
394	**kwargs,
395	):
396	r"""
397	Method for spider plots. Convenience access function to
398	:func:`~pyrolite.plot.spider.spider` (see `Other Parameters`, below), where
399	further parameters for relevant `matplotlib` functions are also listed.
400
401	Parameters
402	----------
403	components : :class:`list`, `None`
404	Elements or compositional components to plot.
405	indexes : :class:`list`, `None`
406	Elements or compositional components to plot.
407	ax : :class:`matplotlib.axes.Axes`, :code:`None`
408	The subplot to draw on.
409	index_order
410	Function to order spider plot indexes (e.g. by incompatibility).
411	autoscale : :class:`bool`
412	Whether to autoscale the y-axis limits for standard spider plots.
413	mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
414	Mode for plot. Plot will produce a line-scatter diagram. Fill will return
415	a filled range. Density will return a conditional density diagram.
416	scatter_kw : :class:`dict`
417	Keyword parameters to be passed to the scatter plotting function.
418	line_kw : :class:`dict`
419	Keyword parameters to be passed to the line plotting function.
420	{otherparams}
421
422	Returns
423	-------
424	:class:`matplotlib.axes.Axes`
425	Axes on which the spider diagram is plotted.
426
427	Todo
428	----
429	* Add 'compositional data' filter for default components if None is given
430
431	"""
432	obj = to_frame(self._obj)	12✔
433
434	if components is None: # default to plotting elemental data	12✔
435	components = [	12✔
436	el for el in obj.columns if el in geochem.ind.common_elements()
437	]
438
439	assert len(components) != 0	12✔
440
441	if index_order is not None:	12✔
UNCOV 442	if isinstance(index_order, str):	×
UNCOV 443	try:	×
444	index_order = geochem.ind.ordering[index_order]	×
445	except KeyError:	×
446	msg = (	×
447	"Ordering not applied, as parameter '{}' not recognized."
448	" Select from: {}"
449	).format(index_order, ", ".join(list(geochem.ind.ordering.keys())))
UNCOV 450	logger.warning(msg)	×
UNCOV 451	components = index_order(components)	×
452	else:
453	components = index_order(components)	×
454
455	ax = init_axes(ax=ax, **kwargs)	12✔
456
457	if hasattr(ax, "_pyrolite_components"):	12✔
458	pass
459
460	ax = spider.spider(	12✔
461	obj.reindex(columns=components).astype(float).values,
462	indexes=indexes,
463	ax=ax,
464	mode=mode,
465	autoscale=autoscale,
466	scatter_kw=scatter_kw,
467	line_kw=line_kw,
468	**kwargs,
469	)
470	ax._pyrolite_components = components	12✔
471	ax.set_xticklabels(components, rotation=60)	12✔
472	return ax	12✔
473
474	def stem(	12✔
475	self,
476	components: list = None,
477	ax=None,
478	orientation="horizontal",
479	axlabels=True,
480	**kwargs,
481	):
482	r"""
483	Method for creating stem plots. Convenience access function to
484	:func:`~pyrolite.plot.stem.stem` (see `Other Parameters`, below), where
485	further parameters for relevant `matplotlib` functions are also listed.
486
487	Parameters
488	----------
489	components : :class:`list`, :code:`None`
490	Elements or compositional components to plot.
491	ax : :class:`matplotlib.axes.Axes`, :code:`None`
492	The subplot to draw on.
493	orientation : :class:`str`
494	Orientation of the plot (horizontal or vertical).
495	axlabels : :class:`bool`, True
496	Whether to add x-y axis labels.
497	{otherparams}
498
499	Returns
500	-------
501	:class:`matplotlib.axes.Axes`
502	Axes on which the stem diagram is plotted.
503	"""
504	obj = to_frame(self._obj)	12✔
505	components = _check_components(obj, components=components, valid_sizes=[2])	12✔
506
507	ax = stem.stem(	12✔
508	*obj.reindex(columns=components).values.T,
509	ax=ax,
510	orientation=orientation,
511	process_color(kwargs),
512	)
513
514	if axlabels:	12✔
515	if "h" not in orientation.lower():	12✔
516	components = components[::-1]	12✔
517	label_axes(ax, labels=components)	12✔
518
519	return ax	12✔
520
521
522	# ideally we would i) check for the same params and ii) aggregate all others across
523	# inherited or chained functions. This simply imports the params from another docstring
524	_add_additional_parameters = True	12✔
525
526	pyroplot.density.__doc__ = pyroplot.density.__doc__.format(	12✔
527	otherparams=[
528	"",
529	get_additional_params(
530	pyroplot.density,
531	density.density,
532	header="Other Parameters",
533	indent=8,
534	subsections=True,
535	),
536	][_add_additional_parameters]
537	)
538
539	pyroplot.parallel.__doc__ = pyroplot.parallel.__doc__.format(	12✔
540	otherparams=[
541	"",
542	get_additional_params(
543	pyroplot.parallel,
544	parallel.parallel,
545	header="Other Parameters",
546	indent=8,
547	subsections=True,
548	),
549	][_add_additional_parameters]
550	)
551
552
553	pyroplot.REE.__doc__ = pyroplot.REE.__doc__.format(	12✔
554	otherparams=[
555	"",
556	get_additional_params(
557	pyroplot.REE,
558	spider.REE_v_radii,
559	header="Other Parameters",
560	indent=8,
561	subsections=True,
562	),
563	][_add_additional_parameters]
564	)
565
566
567	pyroplot.scatter.__doc__ = pyroplot.scatter.__doc__.format(	12✔
568	otherparams=[
569	"",
570	get_additional_params(
571	pyroplot.scatter,
572	plt.scatter,
573	header="Other Parameters",
574	indent=8,
575	subsections=True,
576	),
577	][_add_additional_parameters]
578	)
579
580	pyroplot.plot.__doc__ = pyroplot.plot.__doc__.format(	12✔
581	otherparams=[
582	"",
583	get_additional_params(
584	pyroplot.plot,
585	plt.plot,
586	header="Other Parameters",
587	indent=8,
588	subsections=True,
589	),
590	][_add_additional_parameters]
591	)
592
593	pyroplot.spider.__doc__ = pyroplot.spider.__doc__.format(	12✔
594	otherparams=[
595	"",
596	get_additional_params(
597	pyroplot.spider,
598	spider.spider,
599	header="Other Parameters",
600	indent=8,
601	subsections=True,
602	),
603	][_add_additional_parameters]
604	)
605
606
607	pyroplot.stem.__doc__ = pyroplot.stem.__doc__.format(	12✔
608	otherparams=[
609	"",
610	get_additional_params(
611	pyroplot.stem,
612	stem.stem,
613	header="Other Parameters",
614	indent=8,
615	subsections=True,
616	),
617	][_add_additional_parameters]
618	)
619
620	pyroplot.heatscatter.__doc__ = pyroplot.heatscatter.__doc__.format(	12✔
621	otherparams=[
622	"",
623	get_additional_params(
624	pyroplot.scatter, header="Other Parameters", indent=8, subsections=True
625	),
626	][_add_additional_parameters]
627	)

morganjwilliams / pyrolite / 5564819928

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