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Add quantile feature to forestplot ridgeplot #1047

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merged 7 commits into from
Feb 13, 2020
Merged

Add quantile feature to forestplot ridgeplot #1047

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d1e2f11
Add quantile feature to forestplot ridgeplot
percygautam Feb 5, 2020
7b733f0
Changed the figsize
percygautam Feb 10, 2020
94417f4
added quantile feature to bokeh forestplot
percygautam Feb 12, 2020
155d6cc
changed the figsize of all the ridgeplots(with or without quantiles)
percygautam Feb 12, 2020
a57fd9f
Merge branch 'master' into ridgeplot_quantiles
percygautam Feb 12, 2020
cc9440c
added the change to changelog
percygautam Feb 12, 2020
028b2ff
Merge branch 'master' into ridgeplot_quantiles
percygautam Feb 13, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
* Add `skipna` argument to `hpd` and `summary` (#1035)
* Added `transform` argument to `plot_trace`, `plot_forest`, `plot_pair`, `plot_posterior`, `plot_rank`, `plot_parallel`, `plot_violin`,`plot_density`, `plot_joint` (#1036)
* Add `marker` functionality to `bokeh_plot_elpd` (#1040)
* Add `ridgeplot_quantiles` argument to `plot_forest` (#1047)
* Added the functionality [interactive legends](https://docs.bokeh.org/en/1.4.0/docs/user_guide/interaction/legends.html) for bokeh plots of `densityplot`, `energyplot`
and `essplot` (#1024)

Expand Down
72 changes: 55 additions & 17 deletions arviz/plots/backends/bokeh/forestplot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ def plot_forest(
ridgeplot_overlap,
ridgeplot_alpha,
ridgeplot_kind,
ridgeplot_quantiles,
textsize,
ess,
r_hat,
Expand All @@ -59,7 +60,10 @@ def plot_forest(
)

if figsize is None:
figsize = (min(12, sum(width_ratios) * 2), plot_handler.fig_height())
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ohh, sorry I misread your previous example. This is OK

if kind == "ridgeplot":
figsize = (min(14, sum(width_ratios) * 3), plot_handler.fig_height() * 3)
else:
figsize = (min(12, sum(width_ratios) * 2), plot_handler.fig_height())

(figsize, _, _, _, auto_linewidth, auto_markersize) = _scale_fig_size(figsize, textsize, 1.1, 1)

Expand Down Expand Up @@ -122,7 +126,12 @@ def plot_forest(
)
elif kind == "ridgeplot":
plot_handler.ridgeplot(
ridgeplot_overlap, linewidth, ridgeplot_alpha, ridgeplot_kind, axes[0, 0]
ridgeplot_overlap,
linewidth,
ridgeplot_alpha,
ridgeplot_kind,
ridgeplot_quantiles,
axes[0, 0],
)
else:
raise TypeError(
Expand Down Expand Up @@ -270,7 +279,7 @@ def display_multiple_ropes(self, rope, ax, y, linewidth, rope_var):
)
return ax

def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ax):
def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ridgeplot_quantiles, ax):
"""Draw ridgeplot for each plotter.

Parameters
Expand All @@ -290,7 +299,7 @@ def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ax):
if alpha is None:
alpha = 1.0
for plotter in list(self.plotters.values())[::-1]:
for x, y_min, y_max, color in list(plotter.ridgeplot(mult, ridgeplot_kind))[::-1]:
for x, y_min, y_max, y_q, color in list(plotter.ridgeplot(mult, ridgeplot_kind))[::-1]:
if alpha == 0:
border = color
facecolor = None
Expand All @@ -306,16 +315,43 @@ def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ax):
fill_color=facecolor,
)
else:
patch = ax.patch(
np.concatenate([x, x[::-1]]),
np.concatenate([y_min, y_max[::-1]]),
fill_color=color,
fill_alpha=alpha,
line_dash="solid",
line_width=linewidth,
line_color=border,
)
patch.level = "overlay"
if ridgeplot_quantiles is None:
patch = ax.patch(
np.concatenate([x, x[::-1]]),
np.concatenate([y_min, y_max[::-1]]),
fill_color=color,
fill_alpha=alpha,
line_dash="solid",
line_width=linewidth,
line_color=border,
)
patch.level = "overlay"
else:
quantiles = sorted(np.clip(ridgeplot_quantiles, 0, 1))
if quantiles[0] != 0:
quantiles = [0] + quantiles
if quantiles[-1] != 1:
quantiles = quantiles + [1]

for quant_0, quant_1 in zip(quantiles[:-1], quantiles[1:]):
idx = (y_q > quant_0) & (y_q < quant_1)
if idx.sum():
patch_x = np.concatenate(
(x[idx], [x[idx][-1]], x[idx][::-1], [x[idx][0]])
)
patch_y = np.concatenate(
(
y_min[idx],
[y_min[idx][-1]],
y_max[idx][::-1],
[y_max[idx][0]],
)
)
patch = ax.patch(
patch_x, patch_y, fill_color=color, fill_alpha=alpha,
)
patch.level = "overlay"

return ax

def forestplot(self, credible_interval, quartiles, linewidth, markersize, ax, rope):
Expand Down Expand Up @@ -526,7 +562,7 @@ def treeplot(self, qlist, credible_interval):

def ridgeplot(self, mult, ridgeplot_kind):
"""Get data for each ridgeplot for the variable."""
xvals, yvals, pdfs, colors = [], [], [], []
xvals, yvals, pdfs, pdfs_q, colors = [], [], [], [], []
for y, *_, values, color in self.iterator():
yvals.append(y)
colors.append(color)
Expand All @@ -544,15 +580,17 @@ def ridgeplot(self, mult, ridgeplot_kind):
x = x[:-1]
elif kind == "density":
density, lower, upper = _fast_kde(values)
density_q = density.cumsum() / density.sum()
x = np.linspace(lower, upper, len(density))

xvals.append(x)
pdfs.append(density)
pdfs_q.append((density_q))

scaling = max(np.max(j) for j in pdfs)
for y, x, pdf, color in zip(yvals, xvals, pdfs, colors):
for y, x, pdf, pdf_q, color in zip(yvals, xvals, pdfs, pdfs_q, colors):
y = y * np.ones_like(x)
yield x, y, mult * pdf / scaling + y, color
yield x, y, mult * pdf / scaling + y, pdf_q, color

def ess(self):
"""Get effective n data for the variable."""
Expand Down
43 changes: 33 additions & 10 deletions arviz/plots/backends/matplotlib/forestplot.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ def plot_forest(
ridgeplot_overlap,
ridgeplot_alpha,
ridgeplot_kind,
ridgeplot_quantiles,
textsize,
ess,
r_hat,
Expand All @@ -52,7 +53,10 @@ def plot_forest(
)

if figsize is None:
figsize = (min(12, sum(width_ratios) * 2), plot_handler.fig_height())
if kind == "ridgeplot":
figsize = (min(14, sum(width_ratios) * 4), plot_handler.fig_height() * 1.2)
else:
figsize = (min(12, sum(width_ratios) * 2), plot_handler.fig_height())

(figsize, _, titlesize, xt_labelsize, auto_linewidth, auto_markersize) = _scale_fig_size(
figsize, textsize, 1.1, 1
Expand Down Expand Up @@ -98,7 +102,12 @@ def plot_forest(
)
elif kind == "ridgeplot":
plot_handler.ridgeplot(
ridgeplot_overlap, linewidth, ridgeplot_alpha, ridgeplot_kind, axes[0]
ridgeplot_overlap,
linewidth,
ridgeplot_alpha,
ridgeplot_kind,
ridgeplot_quantiles,
axes[0],
)
else:
raise TypeError(
Expand Down Expand Up @@ -230,7 +239,7 @@ def display_multiple_ropes(self, rope, ax, y, linewidth, rope_var):
)
return ax

def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ax):
def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ridgeplot_quantiles, ax):
"""Draw ridgeplot for each plotter.

Parameters
Expand All @@ -251,7 +260,7 @@ def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ax):
alpha = 1.0
zorder = 0
for plotter in self.plotters.values():
for x, y_min, y_max, color in plotter.ridgeplot(mult, ridgeplot_kind):
for x, y_min, y_max, y_q, color in plotter.ridgeplot(mult, ridgeplot_kind):
if alpha == 0:
border = color
facecolor = "None"
Expand All @@ -269,9 +278,21 @@ def ridgeplot(self, mult, linewidth, alpha, ridgeplot_kind, ax):
zorder=zorder,
)
else:
ax.plot(x, y_max, "-", linewidth=linewidth, color=border, zorder=zorder)
ax.plot(x, y_min, "-", linewidth=linewidth, color=border, zorder=zorder)
ax.fill_between(x, y_min, y_max, alpha=alpha, color=color, zorder=zorder)
if ridgeplot_quantiles is not None:
idx = [np.sum(y_q < quant) for quant in ridgeplot_quantiles]
ax.fill_between(
x,
y_min,
y_max,
where=np.isin(x, x[idx], invert=True, assume_unique=True),
alpha=alpha,
color=color,
zorder=zorder,
)
else:
ax.plot(x, y_max, "-", linewidth=linewidth, color=border, zorder=zorder)
ax.plot(x, y_min, "-", linewidth=linewidth, color=border, zorder=zorder)
ax.fill_between(x, y_min, y_max, alpha=alpha, color=color, zorder=zorder)
zorder -= 1
return ax

Expand Down Expand Up @@ -484,7 +505,7 @@ def treeplot(self, qlist, credible_interval):

def ridgeplot(self, mult, ridgeplot_kind):
"""Get data for each ridgeplot for the variable."""
xvals, yvals, pdfs, colors = [], [], [], []
xvals, yvals, pdfs, pdfs_q, colors = [], [], [], [], []
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this could be

xvals = yvals = pdfs = pdfs_q = colors = []

but it is not that important, so no need to change it

for y, *_, values, color in self.iterator():
yvals.append(y)
colors.append(color)
Expand All @@ -502,15 +523,17 @@ def ridgeplot(self, mult, ridgeplot_kind):
x = x[:-1]
elif kind == "density":
density, lower, upper = _fast_kde(values)
density_q = density.cumsum() / density.sum()
x = np.linspace(lower, upper, len(density))

xvals.append(x)
pdfs.append(density)
pdfs_q.append((density_q))

scaling = max(np.max(j) for j in pdfs)
for y, x, pdf, color in zip(yvals, xvals, pdfs, colors):
for y, x, pdf, pdf_q, color in zip(yvals, xvals, pdfs, pdfs_q, colors):
y = y * np.ones_like(x)
yield x, y, mult * pdf / scaling + y, color
yield x, y, mult * pdf / scaling + y, pdf_q, color

def ess(self):
"""Get effective n data for the variable."""
Expand Down
5 changes: 5 additions & 0 deletions arviz/plots/forestplot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ def plot_forest(
ridgeplot_alpha=None,
ridgeplot_overlap=2,
ridgeplot_kind="auto",
ridgeplot_quantiles=None,
figsize=None,
ax=None,
backend=None,
Expand Down Expand Up @@ -90,6 +91,9 @@ def plot_forest(
ridgeplot_kind : string
By default ("auto") continuous variables are plotted using KDEs and discrete ones using
histograms. To override this use "hist" to plot histograms and "density" for KDEs
ridgeplot_quantiles : list
Quantiles in ascending order used to segment the KDE. Use [.25, .5, .75] for quartiles.
Defaults to None.
figsize : tuple
Figure size. If None it will be defined automatically.
ax: axes, optional
Expand Down Expand Up @@ -188,6 +192,7 @@ def plot_forest(
ridgeplot_overlap=ridgeplot_overlap,
ridgeplot_alpha=ridgeplot_alpha,
ridgeplot_kind=ridgeplot_kind,
ridgeplot_quantiles=ridgeplot_quantiles,
textsize=textsize,
ess=ess,
r_hat=r_hat,
Expand Down