5460340654

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Build # 5460340654

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github

Committed by

morganjwilliams

Commit Message

Merge branch 'release/0.3.3' into main

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97.3

/pyrolite/plot/biplot.py

import numpy as np

from ..comp import codata
from ..util.log import Handle
from ..util.plot.axes import init_axes

logger = Handle(__name__)


def compositional_SVD(X: np.ndarray):
    """
    Breakdown a set of compositions to vertexes and cases for adding to a
    compositional biplot.

    Parameters
    ----------
    X : :class:`numpy.ndarray`
        Compositional array.

    Returns
    ---------
    vertexes, cases : :class:`numpy.ndarray`, :class:`numpy.ndarray`
    """
    U, K, V = np.linalg.svd(codata.CLR(X))
    N = X.shape[1]  # dimensionality
    vertexes = K * V.T / (N - 1) ** 0.5
    cases = (N - 1) ** 0.5 * U.T
    return vertexes, cases


def plot_origin_to_points(
    xs,
    ys,
    labels=None,
    ax=None,
    origin=(0, 0),
    color="k",
    marker="o",
    pad=0.05,
    **kwargs
):
    """
    Plot lines radiating from a specific origin. Fornulated for creation of
    biplots (:func:`covariance_biplot`, :func:`compositional_biplot`).

    Parameters
    -----------
    xs, ys : :class:`numpy.ndarray`
        Coordinates for points to add.
    labels : :class:`list`
        Labels for verticies.
    ax : :class:`matplotlib.axes.Axes`
        Axes to plot on.
    origin : :class:`tuple`
        Origin to plot from.
    color : :class:`str`
        Line color to use.
    marker : :class:`str`
        Marker to use for ends of vectors and origin.
    pad : :class:`float`
        Fraction of vector to pad text label.

    Returns
    --------
    :class:`matplotlib.axes.Axes`
        Axes on which radial plot is added.
    """
    x0, y0 = origin
    ax = init_axes(ax=ax, **kwargs)
    _xs, _ys = (
        np.vstack([x0 * np.ones_like(xs), xs]),
        np.vstack([y0 * np.ones_like(ys), ys]),
    )
    ax.plot(_xs, _ys, color=color, marker=marker, **kwargs)

    if labels is not None:
        for ix, label in enumerate(labels):
            x, y = xs[ix], ys[ix]
            dx, dy = x - x0, y - y0
            theta = np.rad2deg(np.arctan(dy / dx))

            x += pad * dx
            y += pad * dy

            if np.abs(theta) > 60:
                ha = "center"
            else:
                ha = ["right" if x < x0 else "left"][0]

            if np.abs(theta) < 30:
                va = "center"
            else:
                va = ["top" if y < y0 else "bottom"][0]
            ax.annotate(label, (x, y), ha=ha, va=va, rotation=theta)

    return ax


def compositional_biplot(data, labels=None, ax=None, **kwargs):
    """
    Create a compositional biplot.

    Parameters
    -----------
    data : :class:`numpy.ndarray`
        Coordinates for points to add.
    labels : :class:`list`
        Labels for verticies.
    ax : :class:`matplotlib.axes.Axes`
        Axes to plot on.

    Returns
    --------
    :class:`matplotlib.axes.Axes`
        Axes on which biplot is added.
    """

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

    v, c = compositional_SVD(data)
    ax.scatter(*c[:, :2].T, **kwargs)
    plot_origin_to_points(
        *v[:, :2].T,
        ax=ax,
        marker=None,
        labels=labels,
        alpha=0.5,
        zorder=-1,
        label="Variables",
    )
    return ax

1	import numpy as np	12✔
2
3	from ..comp import codata	12✔
4	from ..util.log import Handle	12✔
5	from ..util.plot.axes import init_axes	12✔
6
7	logger = Handle(__name__)	12✔
8
9
10	def compositional_SVD(X: np.ndarray):	12✔
11	"""
12	Breakdown a set of compositions to vertexes and cases for adding to a
13	compositional biplot.
14
15	Parameters
16	----------
17	X : :class:`numpy.ndarray`
18	Compositional array.
19
20	Returns
21	---------
22	vertexes, cases : :class:`numpy.ndarray`, :class:`numpy.ndarray`
23	"""
24	U, K, V = np.linalg.svd(codata.CLR(X))	12✔
25	N = X.shape[1] # dimensionality	12✔
26	vertexes = K * V.T / (N - 1) ** 0.5	12✔
27	cases = (N - 1) ** 0.5 * U.T	12✔
28	return vertexes, cases	12✔
29
30
31	def plot_origin_to_points(	12✔
32	xs,
33	ys,
34	labels=None,
35	ax=None,
36	origin=(0, 0),
37	color="k",
38	marker="o",
39	pad=0.05,
40	**kwargs
41	):
42	"""
43	Plot lines radiating from a specific origin. Fornulated for creation of
44	biplots (:func:`covariance_biplot`, :func:`compositional_biplot`).
45
46	Parameters
47	-----------
48	xs, ys : :class:`numpy.ndarray`
49	Coordinates for points to add.
50	labels : :class:`list`
51	Labels for verticies.
52	ax : :class:`matplotlib.axes.Axes`
53	Axes to plot on.
54	origin : :class:`tuple`
55	Origin to plot from.
56	color : :class:`str`
57	Line color to use.
58	marker : :class:`str`
59	Marker to use for ends of vectors and origin.
60	pad : :class:`float`
61	Fraction of vector to pad text label.
62
63	Returns
64	--------
65	:class:`matplotlib.axes.Axes`
66	Axes on which radial plot is added.
67	"""
68	x0, y0 = origin	12✔
69	ax = init_axes(ax=ax, **kwargs)	12✔
70	_xs, _ys = (	12✔
71	np.vstack([x0 * np.ones_like(xs), xs]),
72	np.vstack([y0 * np.ones_like(ys), ys]),
73	)
74	ax.plot(_xs, _ys, color=color, marker=marker, **kwargs)	12✔
75
76	if labels is not None:	12✔
77	for ix, label in enumerate(labels):	12✔
78	x, y = xs[ix], ys[ix]	12✔
79	dx, dy = x - x0, y - y0	12✔
80	theta = np.rad2deg(np.arctan(dy / dx))	12✔
81
82	x += pad * dx	12✔
83	y += pad * dy	12✔
84
85	if np.abs(theta) > 60:	12✔
UNCOV 86	ha = "center"	×
87	else:
88	ha = ["right" if x < x0 else "left"][0]	12✔
89
90	if np.abs(theta) < 30:	12✔
91	va = "center"	12✔
92	else:
93	va = ["top" if y < y0 else "bottom"][0]	12✔
94	ax.annotate(label, (x, y), ha=ha, va=va, rotation=theta)	12✔
95
96	return ax	12✔
97
98
99	def compositional_biplot(data, labels=None, ax=None, **kwargs):	12✔
100	"""
101	Create a compositional biplot.
102
103	Parameters
104	-----------
105	data : :class:`numpy.ndarray`
106	Coordinates for points to add.
107	labels : :class:`list`
108	Labels for verticies.
109	ax : :class:`matplotlib.axes.Axes`
110	Axes to plot on.
111
112	Returns
113	--------
114	:class:`matplotlib.axes.Axes`
115	Axes on which biplot is added.
116	"""
117
118	ax = init_axes(ax=ax, **kwargs)	12✔
119
120	v, c = compositional_SVD(data)	12✔
121	ax.scatter(c[:, :2].T, *kwargs)	12✔
122	plot_origin_to_points(	12✔
123	*v[:, :2].T,
124	ax=ax,
125	marker=None,
126	labels=labels,
127	alpha=0.5,
128	zorder=-1,
129	label="Variables",
130	)
131	return ax	12✔

morganjwilliams / pyrolite / 5460340654

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