def _scipy_bivariate_kde(x, y, bw, gridsize, cut, clip):
"""Compute a bivariate kde using scipy."""
data = np.c_[x, y]
kde = stats.gaussian_kde(data.T)
if isinstance(bw, str):
bw = "scotts" if bw == "scott" else bw
bw = getattr(kde, "%s_factor" % bw)()
x_support = _kde_support(data[:, 0], bw, gridsize, cut, clip[0])
y_support = _kde_support(data[:, 1], bw, gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde([xx.ravel(), yy.ravel()]).reshape(xx.shape)
return xx, yy, z
def _scipy_bivariate_kde(x, y, bw, gridsize, cut, clip):
"""Compute a bivariate kde using scipy."""
data = np.c_[x, y]
kde = stats.gaussian_kde(data.T)
if isinstance(bw, str):
bw = "scotts" if bw == "scott" else bw
bw = getattr(kde, "%s_factor" % bw)()
x_support = _kde_support(data[:, 0], bw, gridsize, cut, clip[0])
y_support = _kde_support(data[:, 1], bw, gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde([xx.ravel(), yy.ravel()]).reshape(xx.shape)
return xx, yy, z
def _statsmodels_bivariate_kde(x, y, bw, gridsize, cut, clip):
"""Compute a bivariate kde using statsmodels."""
from statsmodels import nonparametric
if isinstance(bw, str):
bw_func = getattr(nonparametric.bandwidths, "bw_" + bw)
x_bw = bw_func(x)
y_bw = bw_func(y)
bw = [x_bw, y_bw]
elif np.isscalar(bw):
bw = [bw, bw]
kde = nonparametric.kernel_density.KDEMultivariate([x, y], "cc", bw)
x_support = _kde_support(x, kde.bw[0], gridsize, cut, clip[0])
y_support = _kde_support(y, kde.bw[1], gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde.pdf([xx.ravel(), yy.ravel()]).reshape(xx.shape)
return xx, yy, z
def _statsmodels_bivariate_kde(x, y, bw, gridsize, cut, clip):
"""Compute a bivariate kde using statsmodels."""
from statsmodels import nonparametric
if isinstance(bw, str):
bw_func = getattr(nonparametric.bandwidths, "bw_" + bw)
x_bw = bw_func(x)
y_bw = bw_func(y)
bw = [x_bw, y_bw]
elif np.isscalar(bw):
bw = [bw, bw]
kde = nonparametric.kernel_density.KDEMultivariate([x, y], "cc", bw)
x_support = _kde_support(x, kde.bw[0], gridsize, cut, clip[0])
y_support = _kde_support(y, kde.bw[1], gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde.pdf([xx.ravel(), yy.ravel()]).reshape(xx.shape)
return xx, yy, z
def _scipy_univariate_kde(data, bw, gridsize, cut, clip):
"""Compute a univariate kernel density estimate using scipy."""
kde = stats.gaussian_kde(data, bw_method=bw)
if isinstance(bw, str):
bw = "scotts" if bw == "scott" else bw
bw = getattr(kde, "%s_factor" % bw)()
grid = _kde_support(data, bw, gridsize, cut, clip)
y = kde(grid)
return grid, y
def _scipy_univariate_kde(data, bw, gridsize, cut, clip):
"""Compute a univariate kernel density estimate using scipy."""
kde = stats.gaussian_kde(data, bw_method=bw)
if isinstance(bw, str):
bw = "scotts" if bw == "scott" else bw
bw = getattr(kde, "%s_factor" % bw)()
grid = _kde_support(data, bw, gridsize, cut, clip)
y = kde(grid)
return grid, y
def _bivariate_kde(x, y, filled, kernel, bw, gridsize, cut, clip, axlabel, ax,
**kwargs):
"""Plot a joint KDE estimate as a bivariate contour plot."""
# Determine the clipping
if clip is None:
clip = [(-np.inf, np.inf), (-np.inf, np.inf)]
elif np.ndim(clip) == 1:
clip = [clip, clip]
# Calculate the KDE
if isinstance(bw, str):
bw_func = getattr(sm.nonparametric.bandwidths, "bw_" + bw)
x_bw = bw_func(x)
y_bw = bw_func(y)
bw = [x_bw, y_bw]
elif np.isscalar(bw):
bw = [bw, bw]
kde = sm.nonparametric.KDEMultivariate([x, y], "cc", bw)
x_support = _kde_support(x, kde.bw[0], gridsize, cut, clip[0])
y_support = _kde_support(y, kde.bw[1], gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde.pdf([xx.ravel(), yy.ravel()]).reshape(xx.shape)
# Plot the contours
n_levels = kwargs.pop("n_levels", 10)
cmap = kwargs.pop("cmap", "BuGn" if filled else "BuGn_d")
if isinstance(cmap, str):
if cmap.endswith("_d"):
pal = ["#333333"]
pal.extend(color_palette(cmap.replace("_d", "_r"), 2))
cmap = blend_palette(pal, as_cmap=True)
contour_func = ax.contourf if filled else ax.contour
contour_func(xx, yy, z, n_levels, cmap=cmap, **kwargs)
# Label the axes
if hasattr(x, "name") and axlabel:
ax.set_xlabel(x.name)
if hasattr(y, "name") and axlabel:
ax.set_ylabel(y.name)
return ax
def kdeplot(a, npts=1000, shade=False, support_thresh=1e-4,
support_min=-np.inf, support_max=np.inf,
vertical=False, ax=None, **kwargs):
"""Calculate and plot kernel density estimate.
Parameters
----------
a : ndarray
input data
npts : int, optional
number of x points
shade : bool, optional
whether to shade under kde curve
support_thresh : float, default 1e-4
draw density for values up to support_thresh * max(density)
support_{min, max}: float, default to (-) inf
if given, do not draw above or below these values
(does not affect the actual estimation)
vertical : bool, defualt False
if True, density is on x-axis
ax : matplotlib axis, optional
axis to plot on, otherwise creates new one
kwargs : other keyword arguments for plot()
Returns
-------
ax : matplotlib axis
axis with plot
"""
if ax is None:
ax = plt.gca()
a = np.asarray(a)
kde = stats.gaussian_kde(a.astype(float).ravel())
x = _kde_support(a, kde, npts, support_thresh)
x = x[x >= support_min]
x = x[x <= support_max]
y = kde(x)
if vertical:
y, x = x, y
line, = ax.plot(x, y, **kwargs)
color = line.get_color()
line.remove()
kwargs.pop("color", None)
ax.plot(x, y, color=color, **kwargs)
if shade:
ax.fill_between(x, 0, y, color=color, alpha=0.25)
return ax
def kdeplot(a, npts=1000, shade=False, support_thresh=1e-4,
support_min=-np.inf, support_max=np.inf,
vertical=False, ax=None, **kwargs):
"""Calculate and plot kernel density estimate.
Parameters
----------
a : ndarray
input data
npts : int, optional
number of x points
shade : bool, optional
whether to shade under kde curve
support_thresh : float, default 1e-4
draw density for values up to support_thresh * max(density)
support_{min, max}: float, default to (-) inf
if given, do not draw above or below these values
(does not affect the actual estimation)
vertical : bool, defualt False
if True, density is on x-axis
ax : matplotlib axis, optional
axis to plot on, otherwise creates new one
kwargs : other keyword arguments for plot()
Returns
-------
ax : matplotlib axis
axis with plot
"""
if ax is None:
ax = plt.gca()
a = np.asarray(a)
kde = stats.gaussian_kde(a.astype(float).ravel())
x = _kde_support(a, kde, npts, support_thresh)
x = x[x >= support_min]
x = x[x <= support_max]
y = kde(x)
if vertical:
y, x = x, y
line, = ax.plot(x, y, **kwargs)
color = line.get_color()
line.remove()
kwargs.pop("color", None)
ax.plot(x, y, color=color, **kwargs)
if shade:
ax.fill_between(x, 0, y, color=color, alpha=0.25)
return ax
def hacked_statsmodels_bivariate_kde(x, y, bw, gridsize, cut, clip):
"""Compute a bivariate kde using statsmodels. Modified to give the exponentiated values on the y axis"""
import statsmodels.nonparametric.api as smnp
from seaborn.utils import _kde_support
if isinstance(bw, str):
bw_func = getattr(smnp.bandwidths, "bw_" + bw)
x_bw = bw_func(x)
y_bw = bw_func(y)
bw = [x_bw, y_bw]
elif np.isscalar(bw):
bw = [bw, bw]
if isinstance(x, pd.Series):
x = x.values
if isinstance(y, pd.Series):
y = y.values
kde = smnp.KDEMultivariate([x, y], "cc", bw)
x_support = _kde_support(x, kde.bw[0], gridsize, cut, clip[0])
y_support = _kde_support(y, kde.bw[1], gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde.pdf([xx.ravel(), yy.ravel()]).reshape(xx.shape)
# exponentiate y values
return xx, np.exp(yy), z
def hacked_statsmodels_bivariate_kde(x, y, bw, gridsize, cut, clip):
"""Compute a bivariate kde using statsmodels. Modified to give the exponentiated values on the y axis"""
import statsmodels.nonparametric.api as smnp
from seaborn.utils import _kde_support
if isinstance(bw, str):
bw_func = getattr(smnp.bandwidths, "bw_" + bw)
x_bw = bw_func(x)
y_bw = bw_func(y)
bw = [x_bw, y_bw]
elif np.isscalar(bw):
bw = [bw, bw]
if isinstance(x, pd.Series):
x = x.values
if isinstance(y, pd.Series):
y = y.values
kde = smnp.KDEMultivariate([x, y], "cc", bw)
x_support = _kde_support(x, kde.bw[0], gridsize, cut, clip[0])
y_support = _kde_support(y, kde.bw[1], gridsize, cut, clip[1])
xx, yy = np.meshgrid(x_support, y_support)
z = kde.pdf([xx.ravel(), yy.ravel()]).reshape(xx.shape)
# exponentiate y values
return xx, np.exp(yy), z
def distplot(a, bins=None, hist=True, kde=True, rug=False, fit=None,
hist_kws=None, kde_kws=None, rug_kws=None, fit_kws=None,
color=None, vertical=False, axlabel=None, ax=None):
"""Flexibly plot a distribution of observations.
Parameter
a : (squeezable to) 1d array
Observed data.
bins : argument for matplotlib hist(), or None
Specification of hist bins, or None to use Freedman-Diaconis rule.
hist : bool, default True
Whether to plot a (normed) histogram.
kde : bool, default True
Whether to plot a gaussian kernel density estimate.
rug : bool, default False
Whether to draw a rugplot on the support axis.
fit : random variable object
An object with `fit` method, returning a tuple that can be passed to a
`pdf` method a positional arguments following an grid of values to
evaluate the pdf on.
{hist, kde, rug, fit}_kws : dictionaries
Keyword arguments for underlying plotting functions.
color : matplotlib color, optional
Color to plot everything but the fitted curve in.
vertical : bool, default False
If True, oberved values are on y-axis.
axlabel : string, False, or None
Name for the support axis label. If None, will try to get it
from a.namel if False, do not set a label.
ax : matplotlib axis, optional
if provided, plot on this axis
Returns
-------
ax : matplotlib axis
"""
if ax is None:
ax = plt.gca()
# Intelligently label the support axis
label_ax = bool(axlabel)
if axlabel is None and hasattr(a, "name"):
axlabel = a.name
if axlabel is not None:
label_ax = True
# Make a a 1-d array
a = np.asarray(a).squeeze()
# Handle dictionary defaults
if hist_kws is None:
hist_kws = dict()
if kde_kws is None:
kde_kws = dict()
if rug_kws is None:
rug_kws = dict()
if fit_kws is None:
fit_kws = dict()
# Get the color from the current color cycle
if color is None:
if vertical:
line, = ax.plot(0, a.mean())
else:
line, = ax.plot(a.mean(), 0)
color = line.get_color()
line.remove()
if hist:
if bins is None:
bins = _freedman_diaconis_bins(a)
hist_alpha = hist_kws.pop("alpha", 0.4)
orientation = "horizontal" if vertical else "vertical"
hist_color = hist_kws.pop("color", color)
ax.hist(a, bins, normed=True, color=hist_color, alpha=hist_alpha,
orientation=orientation, **hist_kws)
if kde:
kde_color = kde_kws.pop("color", color)
kdeplot(a, vertical=vertical, color=kde_color, ax=ax, **kde_kws)
if rug:
rug_color = rug_kws.pop("color", color)
axis = "y" if vertical else "x"
rugplot(a, axis=axis, color=rug_color, ax=ax, **rug_kws)
if fit is not None:
fit_color = fit_kws.pop("color", "#282828")
gridsize = fit_kws.pop("gridsize", 500)
cut = fit_kws.pop("cut", 3)
clip = fit_kws.pop("clip", (-np.inf, np.inf))
bw = sm.nonparametric.bandwidths.bw_scott(a)
x = _kde_support(a, bw, gridsize, cut, clip)
params = fit.fit(a)
pdf = lambda x: fit.pdf(x, *params)
y = pdf(x)
if vertical:
x, y = y, x
ax.plot(x, y, color=fit_color, **fit_kws)
if label_ax:
if vertical:
ax.set_ylabel(axlabel)
else:
ax.set_xlabel(axlabel)
return ax
def distplot(a,
bins=None,
hist=True,
kde=True,
rug=False,
fit=None,
hist_kws=None,
kde_kws=None,
rug_kws=None,
fit_kws=None,
color=None,
vertical=False,
axlabel=None,
ax=None):
"""Flexibly plot a distribution of observations.
Parameter
a : (squeezable to) 1d array
Observed data.
bins : argument for matplotlib hist(), or None
Specification of hist bins, or None to use Freedman-Diaconis rule.
hist : bool, default True
Whether to plot a (normed) histogram.
kde : bool, default True
Whether to plot a gaussian kernel density estimate.
rug : bool, default False
Whether to draw a rugplot on the support axis.
fit : random variable object
An object with `fit` method, returning a tuple that can be passed to a
`pdf` method a positional arguments following an grid of values to
evaluate the pdf on.
{hist, kde, rug, fit}_kws : dictionaries
Keyword arguments for underlying plotting functions.
color : matplotlib color, optional
Color to plot everything but the fitted curve in.
vertical : bool, default False
If True, oberved values are on y-axis.
axlabel : string, False, or None
Name for the support axis label. If None, will try to get it
from a.namel if False, do not set a label.
ax : matplotlib axis, optional
if provided, plot on this axis
Returns
-------
ax : matplotlib axis
"""
if ax is None:
ax = plt.gca()
# Intelligently label the support axis
label_ax = bool(axlabel)
if axlabel is None and hasattr(a, "name"):
axlabel = a.name
if axlabel is not None:
label_ax = True
# Make a a 1-d array
a = np.asarray(a).squeeze()
# Handle dictionary defaults
if hist_kws is None:
hist_kws = dict()
if kde_kws is None:
kde_kws = dict()
if rug_kws is None:
rug_kws = dict()
if fit_kws is None:
fit_kws = dict()
# Get the color from the current color cycle
if color is None:
if vertical:
line, = ax.plot(0, a.mean())
else:
line, = ax.plot(a.mean(), 0)
color = line.get_color()
line.remove()
if hist:
if bins is None:
bins = _freedman_diaconis_bins(a)
hist_alpha = hist_kws.pop("alpha", 0.4)
orientation = "horizontal" if vertical else "vertical"
hist_color = hist_kws.pop("color", color)
ax.hist(a,
bins,
normed=True,
color=hist_color,
alpha=hist_alpha,
orientation=orientation,
**hist_kws)
if kde:
kde_color = kde_kws.pop("color", color)
kdeplot(a, vertical=vertical, color=kde_color, ax=ax, **kde_kws)
if rug:
rug_color = rug_kws.pop("color", color)
axis = "y" if vertical else "x"
rugplot(a, axis=axis, color=rug_color, ax=ax, **rug_kws)
if fit is not None:
fit_color = fit_kws.pop("color", "#282828")
gridsize = fit_kws.pop("gridsize", 500)
cut = fit_kws.pop("cut", 3)
clip = fit_kws.pop("clip", (-np.inf, np.inf))
bw = sm.nonparametric.bandwidths.bw_scott(a)
x = _kde_support(a, bw, gridsize, cut, clip)
params = fit.fit(a)
pdf = lambda x: fit.pdf(x, *params)
y = pdf(x)
if vertical:
x, y = y, x
ax.plot(x, y, color=fit_color, **fit_kws)
if label_ax:
if vertical:
ax.set_ylabel(axlabel)
else:
ax.set_xlabel(axlabel)
return ax
def kdeplot(a,
shade=False,
npts=1000,
support_thresh=1e-4,
support_min=-np.inf,
support_max=np.inf,
vertical=False,
ax=None,
**kwargs):
"""Calculate and plot a one-dimentional kernel density estimate.
Parameters
----------
a : ndarray
Input data.
shade : bool, optional
If true, shade in the area under the KDE curve.
npts : int, optional
Number of points in the evaluation grid.
support_thresh : float, optional
Draw density for values up to support_thresh * max(density).
support_{min, max}: floats, optional
If provided, do not draw above or below these values
(does not affect the actual estimation)
vertical : bool
If True, density is on x-axis.
ax : matplotlib axis, optional
Axis to plot on, otherwise uses current axis.
kwargs : other keyword arguments for plot()
Returns
-------
ax : matplotlib axis
Axis with plot.
"""
if ax is None:
ax = plt.gca()
# Check if a label was specified in the call
label = kwargs.pop("label", None)
# Otherwise check if the data object has a name
if label is None and hasattr(a, "name"):
label = a.name
# Decide if we're going to add a legend
legend = not label is None
label = "_nolegend_" if label is None else label
# Compute the KDE
a = np.asarray(a)
kde = stats.gaussian_kde(a.astype(float).ravel())
x = _kde_support(a, kde, npts, support_thresh)
x = x[x >= support_min]
x = x[x <= support_max]
y = kde(x)
if vertical:
y, x = x, y
# Find a color for the plot in a way that uses the active color cycle
line, = ax.plot(x, y, **kwargs)
color = line.get_color()
line.remove()
kwargs.pop("color", None)
# Draw the KDE plot and, optionally, shade
ax.plot(x, y, color=color, label=label, **kwargs)
if shade:
ax.fill_between(x, 1e-12, y, color=color, alpha=0.25)
# Draw the legend here
if legend:
ax.legend(loc="best")
return ax
def violin(vals, groupby=None, inner="box", color=None, positions=None,
names=None, widths=.8, alpha=None, join_rm=False, kde_thresh=1e-2,
inner_kws=None, ax=None, **kwargs):
"""Create a violin plot (a combination of boxplot and KDE plot).
Parameters
----------
vals : array or sequence of arrays
data to plot
groupby : grouping object
if `vals` is a Series, this is used to group
inner : box | sticks | points
plot quartiles or individual sample values inside violin
color : mpl color, sequence of colors, or seaborn palette name
inner violin colors
positions : number or sequence of numbers
position of first violin or positions of each violin
widths : float
width of each violin at maximum density
alpha : float, optional
transparancy of violin fill
join_rm : boolean, optional
if True, positions in the input arrays are treated as repeated
measures and are joined with a line plot
names : list of strings, optional
names to plot on x axis, otherwise plots numbers
kde_thresh : float, optional
proportion of maximum at which to threshold the KDE curve
inner_kws : dict, optional
keyword arugments for inner plot
ax : matplotlib axis, optional
axis to plot on, otherwise creates new one
Returns
-------
ax : matplotlib axis
axis with violin plot
"""
if ax is None:
ax = plt.gca()
if isinstance(vals, pd.DataFrame):
if names is None:
names = vals.columns
if vals.columns.name is not None:
xlabel = vals.columns.name
else:
xlabel = None
ylabel = None
vals = vals.values
elif isinstance(vals, pd.Series) and groupby is not None:
if hasattr(groupby, "name"):
xlabel = groupby.name
ylabel = vals.name
grouped_vals = pd.groupby(vals, groupby).values
if names is None:
names = grouped_vals.index
vals = grouped_vals.values
else:
xlabel = None
ylabel = None
if hasattr(vals, 'shape'):
if len(vals.shape) == 1:
if hasattr(vals[0], 'shape'):
vals = list(vals)
else:
vals = [vals]
elif len(vals.shape) == 2:
nr, nc = vals.shape
if nr == 1:
vals = [vals]
elif nc == 1:
vals = [vals.ravel()]
else:
vals = [vals[:, i] for i in xrange(nc)]
else:
raise ValueError("Input x can have no more than 2 dimensions")
if not hasattr(vals[0], '__len__'):
vals = [vals]
vals = [np.asarray(a, float) for a in vals]
if color is None:
colors = husl_palette(len(vals), l=.7)
else:
if hasattr(color, "__iter__") and not isinstance(color, tuple):
colors = color
else:
try:
color = mpl.colors.colorConverter.to_rgb(color)
colors = [color for _ in vals]
except ValueError:
colors = color_palette(color, len(vals))
colors = [mpl.colors.colorConverter.to_rgb(c) for c in colors]
colors = [desaturate(c, .7) for c in colors]
light_vals = [colorsys.rgb_to_hls(*c)[1] for c in colors]
l = min(light_vals) * .6
gray = (l, l, l)
if inner_kws is None:
inner_kws = {}
if positions is None:
positions = np.arange(1, len(vals) + 1)
elif not hasattr(positions, "__iter__"):
positions = np.arange(positions, len(vals) + positions)
in_alpha = inner_kws.pop("alpha", .6 if inner == "points" else 1)
in_alpha *= 1 if alpha is None else alpha
in_color = inner_kws.pop("color", gray)
in_marker = inner_kws.pop("marker", ".")
in_lw = inner_kws.pop("lw", 1.5 if inner == "box" else .8)
for i, a in enumerate(vals):
x = positions[i]
kde = stats.gaussian_kde(a)
y = _kde_support(a, kde, 1000, kde_thresh)
dens = kde(y)
scl = 1 / (dens.max() / (widths / 2))
dens *= scl
ax.fill_betweenx(y, x - dens, x + dens, alpha=alpha, color=colors[i])
if inner == "box":
for quant in moss.percentiles(a, [25, 75]):
q_x = kde(quant) * scl
q_x = [x - q_x, x + q_x]
ax.plot(q_x, [quant, quant], color=in_color,
linestyle=":", linewidth=in_lw, **inner_kws)
med = np.median(a)
m_x = kde(med) * scl
m_x = [x - m_x, x + m_x]
ax.plot(m_x, [med, med], color=in_color,
linestyle="--", linewidth=in_lw, **inner_kws)
elif inner == "stick":
x_vals = kde(a) * scl
x_vals = [x - x_vals, x + x_vals]
ax.plot(x_vals, [a, a], color=in_color,
linewidth=in_lw, alpha=in_alpha, **inner_kws)
elif inner == "points":
x_vals = [x for _ in a]
ax.plot(x_vals, a, in_marker, color=in_color,
alpha=in_alpha, mew=0, **inner_kws)
for side in [-1, 1]:
ax.plot((side * dens) + x, y, c=gray, linewidth=1.5)
if join_rm:
ax.plot(range(1, len(vals) + 1), vals,
color=in_color, alpha=2. / 3)
ax.set_xticks(positions)
if names is not None:
if len(vals) != len(names):
raise ValueError("Length of names list must match nuber of bins")
ax.set_xticklabels(names)
ax.set_xlim(positions[0] - .5, positions[-1] + .5)
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
ax.xaxis.grid(False)
return ax
def distplot(a,
bins=None,
hist=True,
kde=True,
rug=False,
fit=None,
hist_kws=None,
kde_kws=None,
rug_kws=None,
fit_kws=None,
color=None,
vertical=False,
xlabel=None,
ax=None):
"""Flexibly plot a distribution of observations.
Parameter
a : (squeezable to) 1d array
Observed data.
bins : argument for matplotlib hist(), or None
Specification of hist bins, or None to use Freedman-Diaconis rule.
hist : bool, default True
Whether to plot a (normed) histogram.
kde : bool, default True
Whether to plot a gaussian kernel density estimate.
rug : bool, default False
Whether to draw a rugplot on the support axis.
fit : random variable object
An object with `fit` method, returning a tuple that can be passed to a
`pdf` method a positional arguments following an grid of values to
evaluate the pdf on.
{hist, kde, rug, fit}_kws : dictionaries
Keyword arguments for underlying plotting functions.
color : matplotlib color, optional
Color to plot everything but the fitted curve in.
vertical : bool, default False
If True, oberved values are on y-axis.
xlabel : string, False, or None
Name for the x axis label. if None, will try to get it from a.name
if False, do not set the x label.
ax : matplotlib axis, optional
if provided, plot on this axis
Returns
-------
ax : matplotlib axis
"""
if ax is None:
ax = plt.gca()
# Intelligently label the axis
label_x = bool(xlabel)
if xlabel is None and hasattr(a, "name"):
xlabel = a.name
if xlabel is not None:
label_x = True
# Make a a 1-d array
a = np.asarray(a).squeeze()
# Handle dictionary defaults
if hist_kws is None:
hist_kws = dict()
if kde_kws is None:
kde_kws = dict()
if rug_kws is None:
rug_kws = dict()
if fit_kws is None:
fit_kws = dict()
# Get the color from the current color cycle
if color is None:
if vertical:
line, = ax.plot(0, a.mean())
else:
line, = ax.plot(a.mean(), 0)
color = line.get_color()
line.remove()
if hist:
if bins is None:
# From http://stats.stackexchange.com/questions/798/
h = 2 * moss.iqr(a) * len(a)**-(1 / 3)
bins = (a.max() - a.min()) / h
hist_alpha = hist_kws.pop("alpha", 0.4)
orientation = "horizontal" if vertical else "vertical"
hist_color = hist_kws.pop("color", color)
ax.hist(a,
bins,
normed=True,
color=hist_color,
alpha=hist_alpha,
orientation=orientation,
**hist_kws)
if kde:
kde_color = kde_kws.pop("color", color)
kdeplot(a, vertical=vertical, color=kde_color, ax=ax, **kde_kws)
if rug:
rug_color = rug_kws.pop("color", color)
axis = "y" if vertical else "x"
rugplot(a, axis=axis, color=rug_color, ax=ax, **rug_kws)
if fit is not None:
fit_color = fit_kws.pop("color", "#282828")
npts = fit_kws.pop("npts", 1000)
support_thresh = fit_kws.pop("support_thresh", 1e-4)
params = fit.fit(a)
pdf = lambda x: fit.pdf(x, *params)
x = _kde_support(a, pdf, npts, support_thresh)
y = pdf(x)
if vertical:
x, y = y, x
ax.plot(x, y, color=fit_color, **fit_kws)
if label_x:
ax.set_xlabel(xlabel)
return ax
def distplot(a, bins=None, hist=True, kde=True, rug=False, fit=None,
hist_kws=None, kde_kws=None, rug_kws=None, fit_kws=None,
color=None, vertical=False, legend=False, xlabel=None, ax=None):
"""Flexibly plot a distribution of observations.
Parameters
----------
a : (squeezable to) 1d array
observed data
bins : argument for matplotlib hist(), or None
specification of bins or None to use Freedman-Diaconis rule
hist : bool, default True
whether to plot a (normed) histogram
kde : bool, defualt True
whether to plot a gaussian kernel density estimate
rug : bool, default False
whether to draw a rugplot on the support axis
fit : random variable object
object with `fit` method returning a tuple that can be
passed to a `pdf` method a positional arguments following
an array of values to evaluate the pdf at
{hist, kde, rug, fit}_kws : dictionaries
keyword arguments for underlying plotting functions
color : matplotlib color, optional
color to plot everything but the fitted curve in
vertical : bool, default False
if True, oberved values are on y-axis
legend : bool, default True
if True, add a legend to the plot with what the plotted lines are
xlabel : string, False, or None
name for the x axis label. if None, will try to get it from a.name
if False, do not set the x label
ax : matplotlib axis, optional
if provided, plot on this axis
Returns
-------
ax : matplotlib axis
"""
if ax is None:
ax = plt.gca()
# Intelligently label the axis
label_x = bool(xlabel)
if xlabel is None and hasattr(a, "name"):
xlabel = a.name
if xlabel is not None:
label_x = True
# Make a a 1-d array
a = np.asarray(a).squeeze()
# Handle dictionary defaults
if hist_kws is None:
hist_kws = dict()
if kde_kws is None:
kde_kws = dict()
if rug_kws is None:
rug_kws = dict()
if fit_kws is None:
fit_kws = dict()
# Get the color from the current color cycle
if color is None:
if vertical:
line, = ax.plot(0, a.mean())
else:
line, = ax.plot(a.mean(), 0)
color = line.get_color()
line.remove()
if hist:
if bins is None:
# From http://stats.stackexchange.com/questions/798/
h = 2 * moss.iqr(a) * len(a) ** -(1 / 3)
bins = (a.max() - a.min()) / h
hist_alpha = hist_kws.pop("alpha", 0.4)
orientation = "horizontal" if vertical else "vertical"
hist_color = hist_kws.pop("color", color)
ax.hist(a, bins, normed=True, color=hist_color, alpha=hist_alpha,
orientation=orientation, **hist_kws)
if kde:
kde_color = kde_kws.pop("color", color)
kde_kws["label"] = "kde"
kdeplot(a, vertical=vertical, color=kde_color, ax=ax, **kde_kws)
if rug:
rug_color = rug_kws.pop("color", color)
axis = "y" if vertical else "x"
rugplot(a, axis=axis, color=rug_color, ax=ax, **rug_kws)
if fit is not None:
fit_color = fit_kws.pop("color", "#282828")
npts = fit_kws.pop("npts", 1000)
support_thresh = fit_kws.pop("support_thresh", 1e-4)
params = fit.fit(a)
pdf = lambda x: fit.pdf(x, *params)
x = _kde_support(a, pdf, npts, support_thresh)
y = pdf(x)
if vertical:
x, y = y, x
fit_kws["label"] = fit.name
ax.plot(x, y, color=fit_color, **fit_kws)
if legend:
ax.legend(loc="best")
if label_x:
ax.set_xlabel(xlabel)
return ax
def violin(vals,
groupby=None,
inner="box",
color=None,
positions=None,
names=None,
widths=.8,
alpha=None,
join_rm=False,
kde_thresh=1e-2,
inner_kws=None,
ax=None,
**kwargs):
"""Create a violin plot (a combination of boxplot and KDE plot).
Parameters
----------
vals : array or sequence of arrays
data to plot
groupby : grouping object
if `vals` is a Series, this is used to group
inner : box | sticks | points
plot quartiles or individual sample values inside violin
color : mpl color, sequence of colors, or seaborn palette name
inner violin colors
positions : number or sequence of numbers
position of first violin or positions of each violin
widths : float
width of each violin at maximum density
alpha : float, optional
transparancy of violin fill
join_rm : boolean, optional
if True, positions in the input arrays are treated as repeated
measures and are joined with a line plot
names : list of strings, optional
names to plot on x axis, otherwise plots numbers
kde_thresh : float, optional
proportion of maximum at which to threshold the KDE curve
inner_kws : dict, optional
keyword arugments for inner plot
ax : matplotlib axis, optional
axis to plot on, otherwise creates new one
Returns
-------
ax : matplotlib axis
axis with violin plot
"""
if ax is None:
ax = plt.gca()
if isinstance(vals, pd.DataFrame):
if names is None:
names = vals.columns
if vals.columns.name is not None:
xlabel = vals.columns.name
else:
xlabel = None
ylabel = None
vals = vals.values
elif isinstance(vals, pd.Series) and groupby is not None:
if hasattr(groupby, "name"):
xlabel = groupby.name
if names is None:
names = np.sort(pd.unique(groupby))
ylabel = vals.name
grouped_vals = pd.groupby(vals, groupby).values
vals = grouped_vals.values
else:
xlabel = None
ylabel = None
if hasattr(vals, 'shape'):
if len(vals.shape) == 1:
if hasattr(vals[0], 'shape'):
vals = list(vals)
else:
vals = [vals]
elif len(vals.shape) == 2:
nr, nc = vals.shape
if nr == 1:
vals = [vals]
elif nc == 1:
vals = [vals.ravel()]
else:
vals = [vals[:, i] for i in xrange(nc)]
else:
raise ValueError("Input x can have no more than 2 dimensions")
if not hasattr(vals[0], '__len__'):
vals = [vals]
vals = [np.asarray(a, float) for a in vals]
if color is None:
colors = husl_palette(len(vals), l=.7)
else:
if hasattr(color, "__iter__") and not isinstance(color, tuple):
colors = color
else:
try:
color = mpl.colors.colorConverter.to_rgb(color)
colors = [color for _ in vals]
except ValueError:
colors = color_palette(color, len(vals))
colors = [mpl.colors.colorConverter.to_rgb(c) for c in colors]
colors = [desaturate(c, .7) for c in colors]
light_vals = [colorsys.rgb_to_hls(*c)[1] for c in colors]
l = min(light_vals) * .6
gray = (l, l, l)
if inner_kws is None:
inner_kws = {}
if positions is None:
positions = np.arange(1, len(vals) + 1)
elif not hasattr(positions, "__iter__"):
positions = np.arange(positions, len(vals) + positions)
in_alpha = inner_kws.pop("alpha", .6 if inner == "points" else 1)
in_alpha *= 1 if alpha is None else alpha
in_color = inner_kws.pop("color", gray)
in_marker = inner_kws.pop("marker", ".")
in_lw = inner_kws.pop("lw", 1.5 if inner == "box" else .8)
for i, a in enumerate(vals):
x = positions[i]
kde = stats.gaussian_kde(a)
y = _kde_support(a, kde, 1000, kde_thresh)
dens = kde(y)
scl = 1 / (dens.max() / (widths / 2))
dens *= scl
ax.fill_betweenx(y, x - dens, x + dens, alpha=alpha, color=colors[i])
if inner == "box":
for quant in moss.percentiles(a, [25, 75]):
q_x = kde(quant) * scl
q_x = [x - q_x, x + q_x]
ax.plot(q_x, [quant, quant],
color=in_color,
linestyle=":",
linewidth=in_lw,
**inner_kws)
med = np.median(a)
m_x = kde(med) * scl
m_x = [x - m_x, x + m_x]
ax.plot(m_x, [med, med],
color=in_color,
linestyle="--",
linewidth=in_lw,
**inner_kws)
elif inner == "stick":
x_vals = kde(a) * scl
x_vals = [x - x_vals, x + x_vals]
ax.plot(x_vals, [a, a],
color=in_color,
linewidth=in_lw,
alpha=in_alpha,
**inner_kws)
elif inner == "points":
x_vals = [x for _ in a]
ax.plot(x_vals,
a,
in_marker,
color=in_color,
alpha=in_alpha,
mew=0,
**inner_kws)
for side in [-1, 1]:
ax.plot((side * dens) + x, y, c=gray, linewidth=1.5)
if join_rm:
ax.plot(range(1, len(vals) + 1), vals, color=in_color, alpha=2. / 3)
ax.set_xticks(positions)
if names is not None:
if len(vals) != len(names):
raise ValueError("Length of names list must match nuber of bins")
ax.set_xticklabels(names)
ax.set_xlim(positions[0] - .5, positions[-1] + .5)
if xlabel is not None:
ax.set_xlabel(xlabel)
if ylabel is not None:
ax.set_ylabel(ylabel)
ax.xaxis.grid(False)
return ax
def kdeplot(a, shade=False, npts=1000, support_thresh=1e-4,
support_min=-np.inf, support_max=np.inf,
vertical=False, ax=None, **kwargs):
"""Calculate and plot a one-dimentional kernel density estimate.
Parameters
----------
a : ndarray
Input data.
shade : bool, optional
If true, shade in the area under the KDE curve.
npts : int, optional
Number of points in the evaluation grid.
support_thresh : float, optional
Draw density for values up to support_thresh * max(density).
support_{min, max}: floats, optional
If provided, do not draw above or below these values
(does not affect the actual estimation)
vertical : bool
If True, density is on x-axis.
ax : matplotlib axis, optional
Axis to plot on, otherwise uses current axis.
kwargs : other keyword arguments for plot()
Returns
-------
ax : matplotlib axis
Axis with plot.
"""
if ax is None:
ax = plt.gca()
# Check if a label was specified in the call
label = kwargs.pop("label", None)
# Otherwise check if the data object has a name
if label is None and hasattr(a, "name"):
label = a.name
# Decide if we're going to add a legend
legend = not label is None
label = "_nolegend_" if label is None else label
# Compute the KDE
a = np.asarray(a)
kde = stats.gaussian_kde(a.astype(float).ravel())
x = _kde_support(a, kde, npts, support_thresh)
x = x[x >= support_min]
x = x[x <= support_max]
y = kde(x)
if vertical:
y, x = x, y
# Find a color for the plot in a way that uses the active color cycle
line, = ax.plot(x, y, **kwargs)
color = line.get_color()
line.remove()
kwargs.pop("color", None)
# Draw the KDE plot and, optionally, shade
ax.plot(x, y, color=color, label=label, **kwargs)
if shade:
ax.fill_between(x, 1e-12, y, color=color, alpha=0.25)
# Draw the legend here
if legend:
ax.legend(loc="best")
return ax