17569144994

Committed 09 Sep 2025 01:39AM UTC coverage: 90.14% (+0.06%) from 90.077%

Build # 17569144994

Build Type

push

github

Committed by

morganjwilliams

Commit Message

Update example for interactive plotting API

Run Details

0 of 30 new or added lines in 2 files covered. (0.0%)

53 existing lines in 6 files now uncovered.

6226 of 6907 relevant lines covered (90.14%)

10.81 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

85.6

/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 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

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

morganjwilliams / pyrolite / 17569144994

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous