17569160869

Committed 09 Sep 2025 01:41AM UTC coverage: 91.465% (-0.1%) from 91.614%

Build # 17569160869

Build Type

push

github

Committed by

morganjwilliams

Commit Message

Add uncertainties, add optional deps for pyproject.toml; WIP demo NB

Run Details

6226 of 6807 relevant lines covered (91.46%)

10.97 hits per line

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

85.07

/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 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

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

morganjwilliams / pyrolite / 17569160869

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