20402260732

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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 AssertionError:
        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"):
            # 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


# 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	6✔
6
7	import matplotlib	6✔
8	import matplotlib.pyplot as plt	6✔
9	import mpltern	6✔
10	import numpy as np	6✔
11	import pandas as pd	6✔
12
13	warnings.filterwarnings("ignore", "Unknown section")	6✔
14
15	from .. import geochem	6✔
16	from ..comp.codata import ILR, close	6✔
17	from ..util.distributions import get_scaler, sample_kde	6✔
18	from ..util.log import Handle	6✔
19	from ..util.meta import get_additional_params, subkwargs	6✔
20	from ..util.pd import to_frame	6✔
21	from ..util.plot.axes import init_axes, label_axes	6✔
22	from ..util.plot.helpers import plot_cooccurence	6✔
23	from ..util.plot.style import _export_nonRCstyles, linekwargs, scatterkwargs	6✔
24	from . import density, parallel, spider, stem	6✔
25	from .color import process_color	6✔
26
27	logger = Handle(__name__)	6✔
28
29	# pyroplot added to __all__ for docs
30	__all__ = ["density", "spider", "pyroplot"]	6✔
31
32
33	def _check_components(obj, components=None, check_size=True, valid_sizes=[2, 3]):	6✔
34	"""
35	Check that the components provided within a dataframe are consistent with the
36	form of plot being used.
37
38	Parameters
39	----------
40	obj : :class:`pandas.DataFrame`
41	Object to check.
42	components : :class:`list`
43	List of components, optionally specified.
44	check_size : :class:`bool`
45	Whether to verify the size of the column index.
46	valid_sizes : :class:`list`
47	Component list lengths which are valid for the plot type.
48
49	Returns
50	-------
51	:class:`list`
52	Components for the plot.
53	"""
54	try:	6✔
55	if check_size and (obj.columns.size not in valid_sizes):	6✔
56	assert len(components) in valid_sizes	6✔
57
58	if components is None:	6✔
59	components = obj.columns.values	6✔
60	except AssertionError:	6✔
UNCOV 61	msg = "Suggest components or provide a slice of the dataframe."	×
UNCOV 62	raise AssertionError(msg)	×
63	return components	6✔
64
65
66	# note that only some of these methods will be valid for series
67	@pd.api.extensions.register_series_accessor("pyroplot")	6✔
68	@pd.api.extensions.register_dataframe_accessor("pyroplot")	6✔
69	class pyroplot(object):	6✔
70	def __init__(self, obj):	6✔
71	"""
72	Custom dataframe accessor for pyrolite plotting.
73
74	Notes
75	-----
76	This accessor enables the coexistence of array-based plotting functions and
77	methods for pandas objects. This enables some separation of concerns.
78	"""
79	self._validate(obj)	6✔
80	self._obj = obj	6✔
81
82	# refresh custom styling on creation?
83	_export_nonRCstyles()	6✔
84
85	@staticmethod	6✔
86	def _validate(obj):	6✔
87	pass	6✔
88
89	def cooccurence(self, ax=None, normalize=True, log=False, colorbar=False, **kwargs):	6✔
90	"""
91	Plot the co-occurence frequency matrix for a given input.
92
93	Parameters
94	----------
95	ax : :class:`matplotlib.axes.Axes`, :code:`None`
96	The subplot to draw on.
97	normalize : :class:`bool`
98	Whether to normalize the cooccurence to compare disparate variables.
99	log : :class:`bool`
100	Whether to take the log of the cooccurence.
101	colorbar : :class:`bool`
102	Whether to append a colorbar.
103
104	Returns
105	-------
106	:class:`matplotlib.axes.Axes`
107	Axes on which the cooccurence plot is added.
108
109	"""
110	obj = to_frame(self._obj)	6✔
111	ax = plot_cooccurence(	6✔
112	obj.values, ax=ax, normalize=normalize, log=log, colorbar=colorbar, **kwargs
113	)
114	ax.set_xticklabels(obj.columns, minor=False, rotation=90)	6✔
115	ax.set_yticklabels(obj.columns, minor=False)	6✔
116	return ax	6✔
117
118	def density(self, components: list = None, ax=None, axlabels=True, **kwargs):	6✔
119	r"""
120	Method for plotting histograms (mode='hist2d'\|'hexbin') or kernel density
121	esitimates from point data. Convenience access function to
122	:func:`~pyrolite.plot.density.density` (see `Other Parameters`, below), where
123	further parameters for relevant `matplotlib` functions are also listed.
124
125	Parameters
126	----------
127	components : :class:`list`, :code:`None`
128	Elements or compositional components to plot.
129	ax : :class:`matplotlib.axes.Axes`, :code:`None`
130	The subplot to draw on.
131	axlabels : :class:`bool`, True
132	Whether to add x-y axis labels.
133
134	{otherparams}
135
136	Returns
137	-------
138	:class:`matplotlib.axes.Axes`
139	Axes on which the density diagram is plotted.
140
141	"""
142	obj = to_frame(self._obj)	6✔
143	components = _check_components(obj, components=components)	6✔
144
145	ax = density.density(	6✔
146	obj.reindex(columns=components).astype(float).values, ax=ax, **kwargs
147	)
148	if axlabels:	6✔
149	label_axes(ax, labels=components)	6✔
150
151	return ax	6✔
152
153	def heatscatter(	6✔
154	self,
155	components: list = None,
156	ax=None,
157	axlabels=True,
158	logx=False,
159	logy=False,
160	**kwargs,
161	):
162	r"""
163	Heatmapped scatter plots using the pyroplot API. See further parameters
164	for `matplotlib.pyplot.scatter` function below.
165
166	Parameters
167	----------
168	components : :class:`list`, :code:`None`
169	Elements or compositional components to plot.
170	ax : :class:`matplotlib.axes.Axes`, :code:`None`
171	The subplot to draw on.
172	axlabels : :class:`bool`, :code:`True`
173	Whether to add x-y axis labels.
174	logx : :class:`bool`, `False`
175	Whether to log-transform x values before the KDE for bivariate plots.
176	logy : :class:`bool`, `False`
177	Whether to log-transform y values before the KDE for bivariate plots.
178
179	{otherparams}
180
181	Returns
182	-------
183	:class:`matplotlib.axes.Axes`
184	Axes on which the heatmapped scatterplot is added.
185
186	"""
187	obj = to_frame(self._obj)	6✔
188	components = _check_components(obj, components=components)	6✔
189	data, samples = (	6✔
190	obj.reindex(columns=components).values,
191	obj.reindex(columns=components).values,
192	)
193	kdetfm = [ # log transforms	6✔
194	get_scaler([None, np.log][logx], [None, np.log][logy]),
195	lambda x: ILR(close(x)),
196	][len(components) == 3]
197	zi = sample_kde(	6✔
198	data, samples, transform=kdetfm, **subkwargs(kwargs, sample_kde)
199	)
200	kwargs.update({"c": zi})	6✔
201	ax = obj.reindex(columns=components).pyroplot.scatter(	6✔
202	ax=ax, axlabels=axlabels, **kwargs
203	)
204	return ax	6✔
205
206	def parallel(	6✔
207	self,
208	components=None,
209	rescale=False,
210	legend=False,
211	ax=None,
212	**kwargs,
213	):
214	"""
215	Create a :func:`pyrolite.plot.parallel.parallel`. coordinate plot from
216	the columns of the :class:`~pandas.DataFrame`.
217
218	Parameters
219	----------
220	components : :class:`list`, :code:`None`
221	Components to use as axes for the plot.
222	rescale : :class:`bool`
223	Whether to rescale values to [-1, 1].
224	legend : :class:`bool`, :code:`False`
225	Whether to include or suppress the legend.
226	ax : :class:`matplotlib.axes.Axes`, :code:`None`
227	The subplot to draw on.
228	{otherparams}
229
230	Returns
231	-------
232	:class:`matplotlib.axes.Axes`
233	Axes on which the parallel coordinates plot is added.
234
235	Todo
236	----
237	* Adapt figure size based on number of columns.
238
239	"""
240
241	obj = to_frame(self._obj)	6✔
242	ax = parallel.parallel(	6✔
243	obj,
244	components=components,
245	rescale=rescale,
246	legend=legend,
247	ax=ax,
248	**kwargs,
249	)
250	return ax	6✔
251
252	def plot(self, components: list = None, ax=None, axlabels=True, **kwargs):	6✔
253	r"""
254	Convenience method for line plots using the pyroplot API. See
255	further parameters for `matplotlib.pyplot.scatter` function below.
256
257	Parameters
258	----------
259	components : :class:`list`, :code:`None`
260	Elements or compositional components to plot.
261	ax : :class:`matplotlib.axes.Axes`, :code:`None`
262	The subplot to draw on.
263	axlabels : :class:`bool`, :code:`True`
264	Whether to add x-y axis labels.
265	{otherparams}
266
267	Returns
268	-------
269	:class:`matplotlib.axes.Axes`
270	Axes on which the plot is added.
271
272	"""
273	obj = to_frame(self._obj)	×
274	components = _check_components(obj, components=components)	×
275	projection = [None, "ternary"][len(components) == 3]	×
276	ax = init_axes(ax=ax, projection=projection, **kwargs)	×
277	kw = linekwargs(kwargs)	×
278	ax.plot(obj.reindex(columns=components).values.T, *kw)	×
279	# if color is multi, could update line colors here
280	if axlabels:	×
281	label_axes(ax, labels=components)	×
282
283	ax.tick_params("both")	×
284	# ax.grid()
285	# ax.set_aspect("equal")
286	return ax	×
287
288	def REE(	6✔
289	self,
290	index="elements",
291	ax=None,
292	mode="plot",
293	dropPm=True,
294	scatter_kw={},
295	line_kw={},
296	**kwargs,
297	):
298	"""Pass the pandas object to :func:`pyrolite.plot.spider.REE_v_radii`.
299
300	Parameters
301	----------
302	ax : :class:`matplotlib.axes.Axes`, :code:`None`
303	The subplot to draw on.
304	index : :class:`str`
305	Whether to plot radii ('radii') on the principal x-axis, or elements
306	('elements').
307	mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
308	Mode for plot. Plot will produce a line-scatter diagram. Fill will return
309	a filled range. Density will return a conditional density diagram.
310	dropPm : :class:`bool`
311	Whether to exclude the (almost) non-existent element Promethium from the REE
312	list.
313	scatter_kw : :class:`dict`
314	Keyword parameters to be passed to the scatter plotting function.
315	line_kw : :class:`dict`
316	Keyword parameters to be passed to the line plotting function.
317	{otherparams}
318
319	Returns
320	-------
321	:class:`matplotlib.axes.Axes`
322	Axes on which the REE plot is added.
323
324	"""
325	obj = to_frame(self._obj)	6✔
326	ree = [i for i in geochem.ind.REE(dropPm=dropPm) if i in obj.columns]	6✔
327
328	ax = spider.REE_v_radii(	6✔
329	obj.reindex(columns=ree).astype(float).values,
330	index=index,
331	ree=ree,
332	mode=mode,
333	ax=ax,
334	scatter_kw=scatter_kw,
335	line_kw=line_kw,
336	**kwargs,
337	)
338	ax.set_ylabel(r"$\mathrm{X / X_{Reference}}$")	6✔
339	return ax	6✔
340
341	def scatter(self, components: list = None, ax=None, axlabels=True, **kwargs):	6✔
342	r"""
343	Convenience method for scatter plots using the pyroplot API. See
344	further parameters for `matplotlib.pyplot.scatter` function below.
345
346	Parameters
347	----------
348	components : :class:`list`, :code:`None`
349	Elements or compositional components to plot.
350	ax : :class:`matplotlib.axes.Axes`, :code:`None`
351	The subplot to draw on.
352	axlabels : :class:`bool`, :code:`True`
353	Whether to add x-y axis labels.
354	{otherparams}
355
356	Returns
357	-------
358	:class:`matplotlib.axes.Axes`
359	Axes on which the scatterplot is added.
360
361	"""
362	obj = to_frame(self._obj)	6✔
363	components = _check_components(obj, components=components)	6✔
364
365	projection = [None, "ternary"][len(components) == 3]	6✔
366	ax = init_axes(ax=ax, projection=projection, **kwargs)	6✔
367	size = obj.index.size	6✔
368	kw = process_color(size=size, **kwargs)	6✔
369	with warnings.catch_warnings():	6✔
370	# ternary transform where points add to zero will give an unnecessary
371	# warning; here we supress it
372	warnings.filterwarnings(	6✔
373	"ignore", message="invalid value encountered in divide"
374	)
375	ax.scatter(obj.reindex(columns=components).values.T, *scatterkwargs(kw))	6✔
376
377	if axlabels:	6✔
378	label_axes(ax, labels=components)	6✔
379
380	ax.tick_params("both")	6✔
381	# ax.grid()
382	# ax.set_aspect("equal")
383	return ax	6✔
384
385	def spider(	6✔
386	self,
387	components: list = None,
388	indexes: list = None,
389	ax=None,
390	mode="plot",
391	index_order=None,
392	autoscale=True,
393	scatter_kw={},
394	line_kw={},
395	**kwargs,
396	):
397	r"""
398	Method for spider plots. Convenience access function to
399	:func:`~pyrolite.plot.spider.spider` (see `Other Parameters`, below), where
400	further parameters for relevant `matplotlib` functions are also listed.
401
402	Parameters
403	----------
404	components : :class:`list`, `None`
405	Elements or compositional components to plot.
406	indexes : :class:`list`, `None`
407	Elements or compositional components to plot.
408	ax : :class:`matplotlib.axes.Axes`, :code:`None`
409	The subplot to draw on.
410	index_order
411	Function to order spider plot indexes (e.g. by incompatibility).
412	autoscale : :class:`bool`
413	Whether to autoscale the y-axis limits for standard spider plots.
414	mode : :class:`str`, :code`["plot", "fill", "binkde", "ckde", "kde", "hist"]`
415	Mode for plot. Plot will produce a line-scatter diagram. Fill will return
416	a filled range. Density will return a conditional density diagram.
417	scatter_kw : :class:`dict`
418	Keyword parameters to be passed to the scatter plotting function.
419	line_kw : :class:`dict`
420	Keyword parameters to be passed to the line plotting function.
421	{otherparams}
422
423	Returns
424	-------
425	:class:`matplotlib.axes.Axes`
426	Axes on which the spider diagram is plotted.
427
428	Todo
429	----
430	* Add 'compositional data' filter for default components if None is given
431
432	"""
433	obj = to_frame(self._obj)	6✔
434
435	if components is None: # default to plotting elemental data	6✔
436	components = [	6✔
437	el for el in obj.columns if el in geochem.ind.common_elements()
438	]
439
440	assert len(components) != 0	6✔
441
442	if index_order is not None:	6✔
443	if isinstance(index_order, str):	×
444	try:	×
445	index_order = geochem.ind.ordering[index_order]	×
446	except KeyError:	×
447	msg = (	×
448	"Ordering not applied, as parameter '{}' not recognized."
449	" Select from: {}"
450	).format(index_order, ", ".join(list(geochem.ind.ordering.keys())))
451	logger.warning(msg)	×
452	components = index_order(components)	×
453	else:
454	components = index_order(components)	×
455
456	ax = init_axes(ax=ax, **kwargs)	6✔
457
458	if hasattr(ax, "_pyrolite_components"):	6✔
459	# TODO: handle spider diagrams which have specified components
460	pass
461
462	ax = spider.spider(	6✔
463	obj.reindex(columns=components).astype(float).values,
464	indexes=indexes,
465	ax=ax,
466	mode=mode,
467	autoscale=autoscale,
468	scatter_kw=scatter_kw,
469	line_kw=line_kw,
470	**kwargs,
471	)
472	ax._pyrolite_components = components	6✔
473	ax.set_xticklabels(components, rotation=60)	6✔
474	return ax	6✔
475
476	def stem(	6✔
477	self,
478	components: list = None,
479	ax=None,
480	orientation="horizontal",
481	axlabels=True,
482	**kwargs,
483	):
484	r"""
485	Method for creating stem plots. Convenience access function to
486	:func:`~pyrolite.plot.stem.stem` (see `Other Parameters`, below), where
487	further parameters for relevant `matplotlib` functions are also listed.
488
489	Parameters
490	----------
491	components : :class:`list`, :code:`None`
492	Elements or compositional components to plot.
493	ax : :class:`matplotlib.axes.Axes`, :code:`None`
494	The subplot to draw on.
495	orientation : :class:`str`
496	Orientation of the plot (horizontal or vertical).
497	axlabels : :class:`bool`, True
498	Whether to add x-y axis labels.
499	{otherparams}
500
501	Returns
502	-------
503	:class:`matplotlib.axes.Axes`
504	Axes on which the stem diagram is plotted.
505	"""
506	obj = to_frame(self._obj)	6✔
507	components = _check_components(obj, components=components, valid_sizes=[2])	6✔
508
509	ax = stem.stem(	6✔
510	*obj.reindex(columns=components).values.T,
511	ax=ax,
512	orientation=orientation,
513	process_color(kwargs),
514	)
515
516	if axlabels:	6✔
517	if "h" not in orientation.lower():	6✔
518	components = components[::-1]	6✔
519	label_axes(ax, labels=components)	6✔
520
521	return ax	6✔
522
523
524	# ideally we would i) check for the same params and ii) aggregate all others across
525	# inherited or chained functions. This simply imports the params from another docstring
526	_add_additional_parameters = True	6✔
527
528	pyroplot.density.__doc__ = pyroplot.density.__doc__.format(	6✔
529	otherparams=[
530	"",
531	get_additional_params(
532	pyroplot.density,
533	density.density,
534	header="Other Parameters",
535	indent=8,
536	subsections=True,
537	),
538	][_add_additional_parameters]
539	)
540
541	pyroplot.parallel.__doc__ = pyroplot.parallel.__doc__.format(	6✔
542	otherparams=[
543	"",
544	get_additional_params(
545	pyroplot.parallel,
546	parallel.parallel,
547	header="Other Parameters",
548	indent=8,
549	subsections=True,
550	),
551	][_add_additional_parameters]
552	)
553
554
555	pyroplot.REE.__doc__ = pyroplot.REE.__doc__.format(	6✔
556	otherparams=[
557	"",
558	get_additional_params(
559	pyroplot.REE,
560	spider.REE_v_radii,
561	header="Other Parameters",
562	indent=8,
563	subsections=True,
564	),
565	][_add_additional_parameters]
566	)
567
568
569	pyroplot.scatter.__doc__ = pyroplot.scatter.__doc__.format(	6✔
570	otherparams=[
571	"",
572	get_additional_params(
573	pyroplot.scatter,
574	plt.scatter,
575	header="Other Parameters",
576	indent=8,
577	subsections=True,
578	),
579	][_add_additional_parameters]
580	)
581
582	pyroplot.plot.__doc__ = pyroplot.plot.__doc__.format(	6✔
583	otherparams=[
584	"",
585	get_additional_params(
586	pyroplot.plot,
587	plt.plot,
588	header="Other Parameters",
589	indent=8,
590	subsections=True,
591	),
592	][_add_additional_parameters]
593	)
594
595	pyroplot.spider.__doc__ = pyroplot.spider.__doc__.format(	6✔
596	otherparams=[
597	"",
598	get_additional_params(
599	pyroplot.spider,
600	spider.spider,
601	header="Other Parameters",
602	indent=8,
603	subsections=True,
604	),
605	][_add_additional_parameters]
606	)
607
608
609	pyroplot.stem.__doc__ = pyroplot.stem.__doc__.format(	6✔
610	otherparams=[
611	"",
612	get_additional_params(
613	pyroplot.stem,
614	stem.stem,
615	header="Other Parameters",
616	indent=8,
617	subsections=True,
618	),
619	][_add_additional_parameters]
620	)
621
622	pyroplot.heatscatter.__doc__ = pyroplot.heatscatter.__doc__.format(	6✔
623	otherparams=[
624	"",
625	get_additional_params(
626	pyroplot.scatter, header="Other Parameters", indent=8, subsections=True
627	),
628	][_add_additional_parameters]
629	)

morganjwilliams / pyrolite / 20402260732

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