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import warnings
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import pandas as pd
import pytest
import numpy.testing as npt
try:
import pandas.testing as pdt
except ImportError:
import pandas.util.testing as pdt
try:
import statsmodels.regression.linear_model as smlm
_no_statsmodels = False
except ImportError:
_no_statsmodels = True
from seaborn import regression as lm
from seaborn.external.version import Version
from seaborn.palettes import color_palette
rs = np.random.RandomState(0)
class TestLinearPlotter:
rs = np.random.RandomState(77)
df = pd.DataFrame(dict(x=rs.normal(size=60),
d=rs.randint(-2, 3, 60),
y=rs.gamma(4, size=60),
s=np.tile(list("abcdefghij"), 6)))
df["z"] = df.y + rs.randn(60)
df["y_na"] = df.y.copy()
df.loc[[10, 20, 30], 'y_na'] = np.nan
def test_establish_variables_from_frame(self):
p = lm._LinearPlotter()
p.establish_variables(self.df, x="x", y="y")
pdt.assert_series_equal(p.x, self.df.x)
pdt.assert_series_equal(p.y, self.df.y)
pdt.assert_frame_equal(p.data, self.df)
def test_establish_variables_from_series(self):
p = lm._LinearPlotter()
p.establish_variables(None, x=self.df.x, y=self.df.y)
pdt.assert_series_equal(p.x, self.df.x)
pdt.assert_series_equal(p.y, self.df.y)
assert p.data is None
def test_establish_variables_from_array(self):
p = lm._LinearPlotter()
p.establish_variables(None,
x=self.df.x.values,
y=self.df.y.values)
npt.assert_array_equal(p.x, self.df.x)
npt.assert_array_equal(p.y, self.df.y)
assert p.data is None
def test_establish_variables_from_lists(self):
p = lm._LinearPlotter()
p.establish_variables(None,
x=self.df.x.values.tolist(),
y=self.df.y.values.tolist())
npt.assert_array_equal(p.x, self.df.x)
npt.assert_array_equal(p.y, self.df.y)
assert p.data is None
def test_establish_variables_from_mix(self):
p = lm._LinearPlotter()
p.establish_variables(self.df, x="x", y=self.df.y)
pdt.assert_series_equal(p.x, self.df.x)
pdt.assert_series_equal(p.y, self.df.y)
pdt.assert_frame_equal(p.data, self.df)
def test_establish_variables_from_bad(self):
p = lm._LinearPlotter()
with pytest.raises(ValueError):
p.establish_variables(None, x="x", y=self.df.y)
def test_dropna(self):
p = lm._LinearPlotter()
p.establish_variables(self.df, x="x", y_na="y_na")
pdt.assert_series_equal(p.x, self.df.x)
pdt.assert_series_equal(p.y_na, self.df.y_na)
p.dropna("x", "y_na")
mask = self.df.y_na.notnull()
pdt.assert_series_equal(p.x, self.df.x[mask])
pdt.assert_series_equal(p.y_na, self.df.y_na[mask])
class TestRegressionPlotter:
rs = np.random.RandomState(49)
grid = np.linspace(-3, 3, 30)
n_boot = 100
bins_numeric = 3
bins_given = [-1, 0, 1]
df = pd.DataFrame(dict(x=rs.normal(size=60),
d=rs.randint(-2, 3, 60),
y=rs.gamma(4, size=60),
s=np.tile(list(range(6)), 10)))
df["z"] = df.y + rs.randn(60)
df["y_na"] = df.y.copy()
bw_err = rs.randn(6)[df.s.values] * 2
df.y += bw_err
p = 1 / (1 + np.exp(-(df.x * 2 + rs.randn(60))))
df["c"] = [rs.binomial(1, p_i) for p_i in p]
df.loc[[10, 20, 30], 'y_na'] = np.nan
def test_variables_from_frame(self):
p = lm._RegressionPlotter("x", "y", data=self.df, units="s")
pdt.assert_series_equal(p.x, self.df.x)
pdt.assert_series_equal(p.y, self.df.y)
pdt.assert_series_equal(p.units, self.df.s)
pdt.assert_frame_equal(p.data, self.df)
def test_variables_from_series(self):
p = lm._RegressionPlotter(self.df.x, self.df.y, units=self.df.s)
npt.assert_array_equal(p.x, self.df.x)
npt.assert_array_equal(p.y, self.df.y)
npt.assert_array_equal(p.units, self.df.s)
assert p.data is None
def test_variables_from_mix(self):
p = lm._RegressionPlotter("x", self.df.y + 1, data=self.df)
npt.assert_array_equal(p.x, self.df.x)
npt.assert_array_equal(p.y, self.df.y + 1)
pdt.assert_frame_equal(p.data, self.df)
def test_variables_must_be_1d(self):
array_2d = np.random.randn(20, 2)
array_1d = np.random.randn(20)
with pytest.raises(ValueError):
lm._RegressionPlotter(array_2d, array_1d)
with pytest.raises(ValueError):
lm._RegressionPlotter(array_1d, array_2d)
def test_dropna(self):
p = lm._RegressionPlotter("x", "y_na", data=self.df)
assert len(p.x) == pd.notnull(self.df.y_na).sum()
p = lm._RegressionPlotter("x", "y_na", data=self.df, dropna=False)
assert len(p.x) == len(self.df.y_na)
@pytest.mark.parametrize("x,y",
[([1.5], [2]),
(np.array([1.5]), np.array([2])),
(pd.Series(1.5), pd.Series(2))])
def test_singleton(self, x, y):
p = lm._RegressionPlotter(x, y)
assert not p.fit_reg
def test_ci(self):
p = lm._RegressionPlotter("x", "y", data=self.df, ci=95)
assert p.ci == 95
assert p.x_ci == 95
p = lm._RegressionPlotter("x", "y", data=self.df, ci=95, x_ci=68)
assert p.ci == 95
assert p.x_ci == 68
p = lm._RegressionPlotter("x", "y", data=self.df, ci=95, x_ci="sd")
assert p.ci == 95
assert p.x_ci == "sd"
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_fast_regression(self):
p = lm._RegressionPlotter("x", "y", data=self.df, n_boot=self.n_boot)
# Fit with the "fast" function, which just does linear algebra
yhat_fast, _ = p.fit_fast(self.grid)
# Fit using the statsmodels function with an OLS model
yhat_smod, _ = p.fit_statsmodels(self.grid, smlm.OLS)
# Compare the vector of y_hat values
npt.assert_array_almost_equal(yhat_fast, yhat_smod)
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_regress_poly(self):
p = lm._RegressionPlotter("x", "y", data=self.df, n_boot=self.n_boot)
# Fit an first-order polynomial
yhat_poly, _ = p.fit_poly(self.grid, 1)
# Fit using the statsmodels function with an OLS model
yhat_smod, _ = p.fit_statsmodels(self.grid, smlm.OLS)
# Compare the vector of y_hat values
npt.assert_array_almost_equal(yhat_poly, yhat_smod)
def test_regress_logx(self):
x = np.arange(1, 10)
y = np.arange(1, 10)
grid = np.linspace(1, 10, 100)
p = lm._RegressionPlotter(x, y, n_boot=self.n_boot)
yhat_lin, _ = p.fit_fast(grid)
yhat_log, _ = p.fit_logx(grid)
assert yhat_lin[0] > yhat_log[0]
assert yhat_log[20] > yhat_lin[20]
assert yhat_lin[90] > yhat_log[90]
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_regress_n_boot(self):
p = lm._RegressionPlotter("x", "y", data=self.df, n_boot=self.n_boot)
# Fast (linear algebra) version
_, boots_fast = p.fit_fast(self.grid)
npt.assert_equal(boots_fast.shape, (self.n_boot, self.grid.size))
# Slower (np.polyfit) version
_, boots_poly = p.fit_poly(self.grid, 1)
npt.assert_equal(boots_poly.shape, (self.n_boot, self.grid.size))
# Slowest (statsmodels) version
_, boots_smod = p.fit_statsmodels(self.grid, smlm.OLS)
npt.assert_equal(boots_smod.shape, (self.n_boot, self.grid.size))
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_regress_without_bootstrap(self):
p = lm._RegressionPlotter("x", "y", data=self.df,
n_boot=self.n_boot, ci=None)
# Fast (linear algebra) version
_, boots_fast = p.fit_fast(self.grid)
assert boots_fast is None
# Slower (np.polyfit) version
_, boots_poly = p.fit_poly(self.grid, 1)
assert boots_poly is None
# Slowest (statsmodels) version
_, boots_smod = p.fit_statsmodels(self.grid, smlm.OLS)
assert boots_smod is None
def test_regress_bootstrap_seed(self):
seed = 200
p1 = lm._RegressionPlotter("x", "y", data=self.df,
n_boot=self.n_boot, seed=seed)
p2 = lm._RegressionPlotter("x", "y", data=self.df,
n_boot=self.n_boot, seed=seed)
_, boots1 = p1.fit_fast(self.grid)
_, boots2 = p2.fit_fast(self.grid)
npt.assert_array_equal(boots1, boots2)
def test_numeric_bins(self):
p = lm._RegressionPlotter(self.df.x, self.df.y)
x_binned, bins = p.bin_predictor(self.bins_numeric)
npt.assert_equal(len(bins), self.bins_numeric)
npt.assert_array_equal(np.unique(x_binned), bins)
def test_provided_bins(self):
p = lm._RegressionPlotter(self.df.x, self.df.y)
x_binned, bins = p.bin_predictor(self.bins_given)
npt.assert_array_equal(np.unique(x_binned), self.bins_given)
def test_bin_results(self):
p = lm._RegressionPlotter(self.df.x, self.df.y)
x_binned, bins = p.bin_predictor(self.bins_given)
assert self.df.x[x_binned == 0].min() > self.df.x[x_binned == -1].max()
assert self.df.x[x_binned == 1].min() > self.df.x[x_binned == 0].max()
def test_scatter_data(self):
p = lm._RegressionPlotter(self.df.x, self.df.y)
x, y = p.scatter_data
npt.assert_array_equal(x, self.df.x)
npt.assert_array_equal(y, self.df.y)
p = lm._RegressionPlotter(self.df.d, self.df.y)
x, y = p.scatter_data
npt.assert_array_equal(x, self.df.d)
npt.assert_array_equal(y, self.df.y)
p = lm._RegressionPlotter(self.df.d, self.df.y, x_jitter=.1)
x, y = p.scatter_data
assert (x != self.df.d).any()
npt.assert_array_less(np.abs(self.df.d - x), np.repeat(.1, len(x)))
npt.assert_array_equal(y, self.df.y)
p = lm._RegressionPlotter(self.df.d, self.df.y, y_jitter=.05)
x, y = p.scatter_data
npt.assert_array_equal(x, self.df.d)
npt.assert_array_less(np.abs(self.df.y - y), np.repeat(.1, len(y)))
def test_estimate_data(self):
p = lm._RegressionPlotter(self.df.d, self.df.y, x_estimator=np.mean)
x, y, ci = p.estimate_data
npt.assert_array_equal(x, np.sort(np.unique(self.df.d)))
npt.assert_array_almost_equal(y, self.df.groupby("d").y.mean())
npt.assert_array_less(np.array(ci)[:, 0], y)
npt.assert_array_less(y, np.array(ci)[:, 1])
def test_estimate_cis(self):
seed = 123
p = lm._RegressionPlotter(self.df.d, self.df.y,
x_estimator=np.mean, ci=95, seed=seed)
_, _, ci_big = p.estimate_data
p = lm._RegressionPlotter(self.df.d, self.df.y,
x_estimator=np.mean, ci=50, seed=seed)
_, _, ci_wee = p.estimate_data
npt.assert_array_less(np.diff(ci_wee), np.diff(ci_big))
p = lm._RegressionPlotter(self.df.d, self.df.y,
x_estimator=np.mean, ci=None)
_, _, ci_nil = p.estimate_data
npt.assert_array_equal(ci_nil, [None] * len(ci_nil))
def test_estimate_units(self):
# Seed the RNG locally
seed = 345
p = lm._RegressionPlotter("x", "y", data=self.df,
units="s", seed=seed, x_bins=3)
_, _, ci_big = p.estimate_data
ci_big = np.diff(ci_big, axis=1)
p = lm._RegressionPlotter("x", "y", data=self.df, seed=seed, x_bins=3)
_, _, ci_wee = p.estimate_data
ci_wee = np.diff(ci_wee, axis=1)
npt.assert_array_less(ci_wee, ci_big)
def test_partial(self):
x = self.rs.randn(100)
y = x + self.rs.randn(100)
z = x + self.rs.randn(100)
p = lm._RegressionPlotter(y, z)
_, r_orig = np.corrcoef(p.x, p.y)[0]
p = lm._RegressionPlotter(y, z, y_partial=x)
_, r_semipartial = np.corrcoef(p.x, p.y)[0]
assert r_semipartial < r_orig
p = lm._RegressionPlotter(y, z, x_partial=x, y_partial=x)
_, r_partial = np.corrcoef(p.x, p.y)[0]
assert r_partial < r_orig
x = pd.Series(x)
y = pd.Series(y)
p = lm._RegressionPlotter(y, z, x_partial=x, y_partial=x)
_, r_partial = np.corrcoef(p.x, p.y)[0]
assert r_partial < r_orig
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_logistic_regression(self):
p = lm._RegressionPlotter("x", "c", data=self.df,
logistic=True, n_boot=self.n_boot)
_, yhat, _ = p.fit_regression(x_range=(-3, 3))
npt.assert_array_less(yhat, 1)
npt.assert_array_less(0, yhat)
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_logistic_perfect_separation(self):
y = self.df.x > self.df.x.mean()
p = lm._RegressionPlotter("x", y, data=self.df,
logistic=True, n_boot=10)
with warnings.catch_warnings():
warnings.simplefilter("ignore", RuntimeWarning)
_, yhat, _ = p.fit_regression(x_range=(-3, 3))
assert np.isnan(yhat).all()
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_robust_regression(self):
p_ols = lm._RegressionPlotter("x", "y", data=self.df,
n_boot=self.n_boot)
_, ols_yhat, _ = p_ols.fit_regression(x_range=(-3, 3))
p_robust = lm._RegressionPlotter("x", "y", data=self.df,
robust=True, n_boot=self.n_boot)
_, robust_yhat, _ = p_robust.fit_regression(x_range=(-3, 3))
assert len(ols_yhat) == len(robust_yhat)
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_lowess_regression(self):
p = lm._RegressionPlotter("x", "y", data=self.df, lowess=True)
grid, yhat, err_bands = p.fit_regression(x_range=(-3, 3))
assert len(grid) == len(yhat)
assert err_bands is None
def test_regression_options(self):
with pytest.raises(ValueError):
lm._RegressionPlotter("x", "y", data=self.df,
lowess=True, order=2)
with pytest.raises(ValueError):
lm._RegressionPlotter("x", "y", data=self.df,
lowess=True, logistic=True)
def test_regression_limits(self):
f, ax = plt.subplots()
ax.scatter(self.df.x, self.df.y)
p = lm._RegressionPlotter("x", "y", data=self.df)
grid, _, _ = p.fit_regression(ax)
xlim = ax.get_xlim()
assert grid.min() == xlim[0]
assert grid.max() == xlim[1]
p = lm._RegressionPlotter("x", "y", data=self.df, truncate=True)
grid, _, _ = p.fit_regression()
assert grid.min() == self.df.x.min()
assert grid.max() == self.df.x.max()
class TestRegressionPlots:
rs = np.random.RandomState(56)
df = pd.DataFrame(dict(x=rs.randn(90),
y=rs.randn(90) + 5,
z=rs.randint(0, 1, 90),
g=np.repeat(list("abc"), 30),
h=np.tile(list("xy"), 45),
u=np.tile(np.arange(6), 15)))
bw_err = rs.randn(6)[df.u.values]
df.y += bw_err
def test_regplot_basic(self):
f, ax = plt.subplots()
lm.regplot(x="x", y="y", data=self.df)
assert len(ax.lines) == 1
assert len(ax.collections) == 2
x, y = ax.collections[0].get_offsets().T
npt.assert_array_equal(x, self.df.x)
npt.assert_array_equal(y, self.df.y)
def test_regplot_selective(self):
f, ax = plt.subplots()
ax = lm.regplot(x="x", y="y", data=self.df, scatter=False, ax=ax)
assert len(ax.lines) == 1
assert len(ax.collections) == 1
ax.clear()
f, ax = plt.subplots()
ax = lm.regplot(x="x", y="y", data=self.df, fit_reg=False)
assert len(ax.lines) == 0
assert len(ax.collections) == 1
ax.clear()
f, ax = plt.subplots()
ax = lm.regplot(x="x", y="y", data=self.df, ci=None)
assert len(ax.lines) == 1
assert len(ax.collections) == 1
ax.clear()
def test_regplot_scatter_kws_alpha(self):
f, ax = plt.subplots()
color = np.array([[0.3, 0.8, 0.5, 0.5]])
ax = lm.regplot(x="x", y="y", data=self.df,
scatter_kws={'color': color})
assert ax.collections[0]._alpha is None
assert ax.collections[0]._facecolors[0, 3] == 0.5
f, ax = plt.subplots()
color = np.array([[0.3, 0.8, 0.5]])
ax = lm.regplot(x="x", y="y", data=self.df,
scatter_kws={'color': color})
assert ax.collections[0]._alpha == 0.8
f, ax = plt.subplots()
color = np.array([[0.3, 0.8, 0.5]])
ax = lm.regplot(x="x", y="y", data=self.df,
scatter_kws={'color': color, 'alpha': 0.4})
assert ax.collections[0]._alpha == 0.4
f, ax = plt.subplots()
color = 'r'
ax = lm.regplot(x="x", y="y", data=self.df,
scatter_kws={'color': color})
assert ax.collections[0]._alpha == 0.8
f, ax = plt.subplots()
alpha = .3
ax = lm.regplot(x="x", y="y", data=self.df,
x_bins=5, fit_reg=False,
scatter_kws={"alpha": alpha})
for line in ax.lines:
assert line.get_alpha() == alpha
def test_regplot_binned(self):
ax = lm.regplot(x="x", y="y", data=self.df, x_bins=5)
assert len(ax.lines) == 6
assert len(ax.collections) == 2
def test_lmplot_no_data(self):
with pytest.raises(TypeError):
# keyword argument `data` is required
lm.lmplot(x="x", y="y")
def test_lmplot_basic(self):
g = lm.lmplot(x="x", y="y", data=self.df)
ax = g.axes[0, 0]
assert len(ax.lines) == 1
assert len(ax.collections) == 2
x, y = ax.collections[0].get_offsets().T
npt.assert_array_equal(x, self.df.x)
npt.assert_array_equal(y, self.df.y)
def test_lmplot_hue(self):
g = lm.lmplot(x="x", y="y", data=self.df, hue="h")
ax = g.axes[0, 0]
assert len(ax.lines) == 2
assert len(ax.collections) == 4
def test_lmplot_markers(self):
g1 = lm.lmplot(x="x", y="y", data=self.df, hue="h", markers="s")
assert g1.hue_kws == {"marker": ["s", "s"]}
g2 = lm.lmplot(x="x", y="y", data=self.df, hue="h", markers=["o", "s"])
assert g2.hue_kws == {"marker": ["o", "s"]}
with pytest.raises(ValueError):
lm.lmplot(x="x", y="y", data=self.df, hue="h",
markers=["o", "s", "d"])
def test_lmplot_marker_linewidths(self):
g = lm.lmplot(x="x", y="y", data=self.df, hue="h",
fit_reg=False, markers=["o", "+"])
c = g.axes[0, 0].collections
assert c[1].get_linewidths()[0] == mpl.rcParams["lines.linewidth"]
def test_lmplot_facets(self):
g = lm.lmplot(x="x", y="y", data=self.df, row="g", col="h")
assert g.axes.shape == (3, 2)
g = lm.lmplot(x="x", y="y", data=self.df, col="u", col_wrap=4)
assert g.axes.shape == (6,)
g = lm.lmplot(x="x", y="y", data=self.df, hue="h", col="u")
assert g.axes.shape == (1, 6)
def test_lmplot_hue_col_nolegend(self):
g = lm.lmplot(x="x", y="y", data=self.df, col="h", hue="h")
assert g._legend is None
def test_lmplot_scatter_kws(self):
g = lm.lmplot(x="x", y="y", hue="h", data=self.df, ci=None)
red_scatter, blue_scatter = g.axes[0, 0].collections
red, blue = color_palette(n_colors=2)
npt.assert_array_equal(red, red_scatter.get_facecolors()[0, :3])
npt.assert_array_equal(blue, blue_scatter.get_facecolors()[0, :3])
@pytest.mark.skipif(Version(mpl.__version__) < Version("3.4"),
reason="MPL bug #15967")
@pytest.mark.parametrize("sharex", [True, False])
def test_lmplot_facet_truncate(self, sharex):
g = lm.lmplot(
data=self.df, x="x", y="y", hue="g", col="h",
truncate=False, facet_kws=dict(sharex=sharex),
)
for ax in g.axes.flat:
for line in ax.lines:
xdata = line.get_xdata()
assert ax.get_xlim() == tuple(xdata[[0, -1]])
def test_lmplot_sharey(self):
df = pd.DataFrame(dict(
x=[0, 1, 2, 0, 1, 2],
y=[1, -1, 0, -100, 200, 0],
z=["a", "a", "a", "b", "b", "b"],
))
with pytest.warns(UserWarning):
g = lm.lmplot(data=df, x="x", y="y", col="z", sharey=False)
ax1, ax2 = g.axes.flat
assert ax1.get_ylim()[0] > ax2.get_ylim()[0]
assert ax1.get_ylim()[1] < ax2.get_ylim()[1]
def test_lmplot_facet_kws(self):
xlim = -4, 20
g = lm.lmplot(
data=self.df, x="x", y="y", col="h", facet_kws={"xlim": xlim}
)
for ax in g.axes.flat:
assert ax.get_xlim() == xlim
def test_residplot(self):
x, y = self.df.x, self.df.y
ax = lm.residplot(x=x, y=y)
resid = y - np.polyval(np.polyfit(x, y, 1), x)
x_plot, y_plot = ax.collections[0].get_offsets().T
npt.assert_array_equal(x, x_plot)
npt.assert_array_almost_equal(resid, y_plot)
@pytest.mark.skipif(_no_statsmodels, reason="no statsmodels")
def test_residplot_lowess(self):
ax = lm.residplot(x="x", y="y", data=self.df, lowess=True)
assert len(ax.lines) == 2
x, y = ax.lines[1].get_xydata().T
npt.assert_array_equal(x, np.sort(self.df.x))
def test_three_point_colors(self):
x, y = np.random.randn(2, 3)
ax = lm.regplot(x=x, y=y, color=(1, 0, 0))
color = ax.collections[0].get_facecolors()
npt.assert_almost_equal(color[0, :3],
(1, 0, 0))
def test_regplot_xlim(self):
f, ax = plt.subplots()
x, y1, y2 = np.random.randn(3, 50)
lm.regplot(x=x, y=y1, truncate=False)
lm.regplot(x=x, y=y2, truncate=False)
line1, line2 = ax.lines
assert np.array_equal(line1.get_xdata(), line2.get_xdata())
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