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Violinplot: fix histogram, add rug #997

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Jan 20, 2020
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Violinplot: fix histogram, add rug #997

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622a5f2
fix histogram, add rug
aloctavodia Jan 14, 2020
a166bb2
add rug to bokeh
aloctavodia Jan 15, 2020
af4aeb8
remove redundant line, make bokeh plot looks closer to matplotlib, fi…
aloctavodia Jan 15, 2020
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58 changes: 42 additions & 16 deletions arviz/plots/backends/bokeh/violinplot.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,12 @@ def plot_violin(
figsize,
rows,
cols,
sharex,
sharey,
kwargs_shade,
shade_kwargs,
shade,
rug,
rug_kwargs,
bw,
credible_interval,
linewidth,
Expand All @@ -40,6 +43,7 @@ def plot_violin(
len(plotters),
rows,
cols,
sharex=sharex,
sharey=sharey,
figsize=figsize,
squeeze=False,
Expand All @@ -54,17 +58,30 @@ def plot_violin(
):
val = x.flatten()
if val[0].dtype.kind == "i":
cat_hist(val, shade, ax_, **kwargs_shade)
dens = cat_hist(val, rug, shade, ax_, **shade_kwargs)
else:
_violinplot(val, shade, bw, ax_, **kwargs_shade)
dens = _violinplot(val, rug, shade, bw, ax_, **shade_kwargs)

if rug:
rug_x = -np.abs(np.random.normal(scale=max(dens) / 3.5, size=len(val)))
ax_.scatter(rug_x, val, **rug_kwargs)

per = np.percentile(val, [25, 75, 50])
hpd_intervals = hpd(val, credible_interval, multimodal=False)

if quartiles:
ax_.line([0, 0], per[:2], line_width=linewidth * 3, line_color="black")
ax_.line([0, 0], hpd_intervals, line_width=linewidth, line_color="black")
ax_.circle(0, per[-1])
ax_.line(
[0, 0], per[:2], line_width=linewidth * 3, line_color="black", line_cap="round"
)
ax_.line([0, 0], hpd_intervals, line_width=linewidth, line_color="black", line_cap="round")
ax_.circle(
0,
per[-1],
line_color="white",
fill_color="white",
size=linewidth * 1.5,
line_width=linewidth,
)

_title = Title()
_title.text = make_label(var_name, selection)
Expand All @@ -80,35 +97,44 @@ def plot_violin(
return ax


def _violinplot(val, shade, bw, ax, **kwargs_shade):
def _violinplot(val, rug, shade, bw, ax, **shade_kwargs):
"""Auxiliary function to plot violinplots."""
density, low_b, up_b = _fast_kde(val, bw=bw)
x = np.linspace(low_b, up_b, len(density))

x = np.concatenate([x, x[::-1]])
density = np.concatenate([-density, density[::-1]])
if not rug:
x = np.concatenate([x, x[::-1]])
density = np.concatenate([-density, density[::-1]])

ax.harea(y=x, x1=density, x2=np.zeros_like(density), fill_alpha=shade, **shade_kwargs)

ax.patch(density, x, fill_alpha=shade, line_width=0, **kwargs_shade)
return density


def cat_hist(val, shade, ax, **kwargs_shade):
def cat_hist(val, rug, shade, ax, **shade_kwargs):
"""Auxiliary function to plot discrete-violinplots."""
bins = get_bins(val)
_, binned_d, _ = histogram(val, bins=bins)

bin_edges = np.linspace(np.min(val), np.max(val), len(bins))
centers = 0.5 * (bin_edges + np.roll(bin_edges, 1))[:-1]
heights = np.diff(bin_edges)
centers = bin_edges[:-1] + heights.mean() / 2
right = 0.5 * binned_d

lefts = -0.5 * binned_d
if rug:
left = 0
else:
left = -right

ax.hbar(
y=centers,
left=lefts,
right=-lefts,
left=left,
right=right,
height=heights,
fill_alpha=shade,
line_alpha=shade,
line_color=None,
**kwargs_shade
**shade_kwargs
)

return binned_d
41 changes: 29 additions & 12 deletions arviz/plots/backends/matplotlib/violinplot.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,12 @@ def plot_violin(
figsize,
rows,
cols,
sharex,
sharey,
kwargs_shade,
shade_kwargs,
shade,
rug,
rug_kwargs,
bw,
credible_interval,
linewidth,
Expand All @@ -29,24 +32,31 @@ def plot_violin(
):
"""Matplotlib violin plot."""
if ax is None:
_, ax = _create_axes_grid(
fig, ax = _create_axes_grid(
len(plotters),
rows,
cols,
sharex=sharex,
sharey=sharey,
figsize=figsize,
squeeze=False,
backend_kwargs=backend_kwargs,
)
fig.set_constrained_layout(False)
fig.subplots_adjust(wspace=0)

ax = np.atleast_1d(ax)

for (var_name, selection, x), ax_ in zip(plotters, ax.flatten()):
val = x.flatten()
if val[0].dtype.kind == "i":
cat_hist(val, shade, ax_, **kwargs_shade)
dens = cat_hist(val, rug, shade, ax_, **shade_kwargs)
else:
_violinplot(val, shade, bw, ax_, **kwargs_shade)
dens = _violinplot(val, rug, shade, bw, ax_, **shade_kwargs)

if rug:
rug_x = -np.abs(np.random.normal(scale=max(dens) / 3.5, size=len(val)))
ax_.plot(rug_x, val, **rug_kwargs)

per = np.percentile(val, [25, 75, 50])
hpd_intervals = hpd(val, credible_interval, multimodal=False)
Expand All @@ -67,25 +77,32 @@ def plot_violin(
return ax


def _violinplot(val, shade, bw, ax, **kwargs_shade):
def _violinplot(val, rug, shade, bw, ax, **shade_kwargs):
"""Auxiliary function to plot violinplots."""
density, low_b, up_b = _fast_kde(val, bw=bw)
x = np.linspace(low_b, up_b, len(density))

x = np.concatenate([x, x[::-1]])
density = np.concatenate([-density, density[::-1]])
if not rug:
x = np.concatenate([x, x[::-1]])
density = np.concatenate([-density, density[::-1]])

ax.fill_betweenx(x, density, alpha=shade, lw=0, **kwargs_shade)
ax.fill_betweenx(x, density, alpha=shade, lw=0, **shade_kwargs)
return density


def cat_hist(val, shade, ax, **kwargs_shade):
def cat_hist(val, rug, shade, ax, **shade_kwargs):
"""Auxiliary function to plot discrete-violinplots."""
bins = get_bins(val)
_, binned_d, _ = histogram(val, bins=bins)

bin_edges = np.linspace(np.min(val), np.max(val), len(bins))
centers = 0.5 * (bin_edges + np.roll(bin_edges, 1))[:-1]
heights = np.diff(bin_edges)
centers = bin_edges[:-1] + heights.mean() / 2

if rug:
left = None
else:
left = -0.5 * binned_d

lefts = -0.5 * binned_d
ax.barh(centers, binned_d, height=heights, left=lefts, alpha=shade, **kwargs_shade)
ax.barh(centers, binned_d, height=heights, left=left, alpha=shade, **shade_kwargs)
return binned_d
35 changes: 29 additions & 6 deletions arviz/plots/violinplot.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,17 @@ def plot_violin(
data,
var_names=None,
quartiles=True,
rug=False,
credible_interval=0.94,
shade=0.35,
bw=4.5,
sharex=True,
sharey=True,
figsize=None,
textsize=None,
ax=None,
kwargs_shade=None,
shade_kwargs=None,
rug_kwargs=None,
backend=None,
backend_kwargs=None,
show=None,
Expand All @@ -42,6 +45,8 @@ def plot_violin(
quartiles : bool, optional
Flag for plotting the interquartile range, in addition to the credible_interval*100%
intervals. Defaults to True
rug : bool
If True adds a jittered rugplot. Defaults to False.
credible_interval : float, optional
Credible intervals. Defaults to 0.94.
shade : float
Expand All @@ -56,12 +61,17 @@ def plot_violin(
textsize: int
Text size of the point_estimates, axis ticks, and HPD. If None it will be autoscaled
based on figsize.
sharex : bool
Defaults to True, violinplots share a common x-axis scale.
sharey : bool
Defaults to True, violinplots share a common y-axis scale.
ax: axes, optional
Matplotlib axes or bokeh figures.
kwargs_shade : dicts, optional
shade_kwargs : dicts, optional
Additional keywords passed to `fill_between`, or `barh` to control the shade.
rug_kwargs : dict
Keywords passed to the rug plot. If true only the righ half side of the violin will be
plotted.
backend: str, optional
Select plotting backend {"matplotlib","bokeh"}. Default "matplotlib".
backend_kwargs: bool, optional
Expand All @@ -81,25 +91,30 @@ def plot_violin(
list(xarray_var_iter(data, var_names=var_names, combined=True)), "plot_violin"
)

if kwargs_shade is None:
kwargs_shade = {}
if shade_kwargs is None:
shade_kwargs = {}

rows, cols = default_grid(len(plotters))

(figsize, ax_labelsize, _, xt_labelsize, linewidth, _) = _scale_fig_size(
figsize, textsize, rows, cols
)
ax_labelsize *= 2

if rug_kwargs is None:
rug_kwargs = {}

violinplot_kwargs = dict(
ax=ax,
plotters=plotters,
figsize=figsize,
rows=rows,
cols=cols,
sharex=sharex,
sharey=sharey,
kwargs_shade=kwargs_shade,
shade_kwargs=shade_kwargs,
shade=shade,
rug=rug,
rug_kwargs=rug_kwargs,
bw=bw,
credible_interval=credible_interval,
linewidth=linewidth,
Expand All @@ -115,6 +130,14 @@ def plot_violin(
violinplot_kwargs.pop("ax_labelsize")
violinplot_kwargs.pop("xt_labelsize")

rug_kwargs.setdefault("fill_alpha", 0.1)
rug_kwargs.setdefault("line_alpha", 0.1)

else:
rug_kwargs.setdefault("alpha", 0.1)
rug_kwargs.setdefault("marker", ".")
rug_kwargs.setdefault("linestyle", "")

# TODO: Add backend kwargs
plot = get_plotting_function("plot_violin", "violinplot", backend)
ax = plot(**violinplot_kwargs)
Expand Down