Seaborn: Color handling error for masked data since Matplotlib 3.1.0

[tomyun]

I'm on Seaborn 0.9.0.

import seaborn as sns
df = sns.load_dataset("exercise")
# intentionally remove some points
df = df.drop(df.query("kind == 'walking' & time == '1 min'").index)
sns.catplot(x="time", y="pulse", hue="kind", kind='point', data=df)

With Matplotlib 3.0.2:

With Matplotlib 3.1.0:

ValueError                                Traceback (most recent call last)
<ipython-input-3-0ddfdcca1938> in <module>
      1 df = sns.load_dataset("exercise")
      2 df = df.drop(df.query("kind == 'walking' & time == '1 min'").index)
----> 3 sns.catplot(x="time", y="pulse", hue="kind", kind='point', data=df)

/usr/local/lib/python3.7/site-packages/seaborn/categorical.py in catplot(x, y, hue, data, row, col, col_wrap, estimator, ci, n_boot, units, order, hue_order, row_order, col_order, kind, height, aspect, orient, color, palette, legend, legend_out, sharex, sharey, margin_titles, facet_kws, **kwargs)
   3753 
   3754     # Draw the plot onto the facets
-> 3755     g.map_dataframe(plot_func, x, y, hue, **plot_kws)
   3756 
   3757     # Special case axis labels for a count type plot

/usr/local/lib/python3.7/site-packages/seaborn/axisgrid.py in map_dataframe(self, func, *args, **kwargs)
    818 
    819             # Draw the plot
--> 820             self._facet_plot(func, ax, args, kwargs)
    821 
    822         # Finalize the annotations and layout

/usr/local/lib/python3.7/site-packages/seaborn/axisgrid.py in _facet_plot(self, func, ax, plot_args, plot_kwargs)
    836 
    837         # Draw the plot
--> 838         func(*plot_args, **plot_kwargs)
    839 
    840         # Sort out the supporting information

/usr/local/lib/python3.7/site-packages/seaborn/categorical.py in pointplot(x, y, hue, data, order, hue_order, estimator, ci, n_boot, units, markers, linestyles, dodge, join, scale, orient, color, palette, errwidth, capsize, ax, **kwargs)
   3338         ax = plt.gca()
   3339 
-> 3340     plotter.plot(ax)
   3341     return ax
   3342 

/usr/local/lib/python3.7/site-packages/seaborn/categorical.py in plot(self, ax)
   1809     def plot(self, ax):
   1810         """Make the plot."""
-> 1811         self.draw_points(ax)
   1812         self.annotate_axes(ax)
   1813         if self.orient == "h":

/usr/local/lib/python3.7/site-packages/seaborn/categorical.py in draw_points(self, ax)
   1805                            c=point_colors, edgecolor=point_colors,
   1806                            linewidth=mew, marker=marker, s=markersize,
-> 1807                            zorder=z)
   1808 
   1809     def plot(self, ax):

/usr/local/lib/python3.7/site-packages/matplotlib/__init__.py in inner(ax, data, *args, **kwargs)
   1587     def inner(ax, *args, data=None, **kwargs):
   1588         if data is None:
-> 1589             return func(ax, *map(sanitize_sequence, args), **kwargs)
   1590 
   1591         bound = new_sig.bind(ax, *args, **kwargs)

/usr/local/lib/python3.7/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, plotnonfinite, **kwargs)
   4488                 offsets=offsets,
   4489                 transOffset=kwargs.pop('transform', self.transData),
-> 4490                 alpha=alpha
   4491                 )
   4492         collection.set_transform(mtransforms.IdentityTransform())

/usr/local/lib/python3.7/site-packages/matplotlib/collections.py in __init__(self, paths, sizes, **kwargs)
    881         """
    882 
--> 883         Collection.__init__(self, **kwargs)
    884         self.set_paths(paths)
    885         self.set_sizes(sizes)

/usr/local/lib/python3.7/site-packages/matplotlib/collections.py in __init__(self, edgecolors, facecolors, linewidths, linestyles, capstyle, joinstyle, antialiaseds, offsets, transOffset, norm, cmap, pickradius, hatch, urls, offset_position, zorder, **kwargs)
    126         self._hatch_color = mcolors.to_rgba(mpl.rcParams['hatch.color'])
    127         self.set_facecolor(facecolors)
--> 128         self.set_edgecolor(edgecolors)
    129         self.set_linewidth(linewidths)
    130         self.set_linestyle(linestyles)

/usr/local/lib/python3.7/site-packages/matplotlib/collections.py in set_edgecolor(self, c)
    726         """
    727         self._original_edgecolor = c
--> 728         self._set_edgecolor(c)
    729 
    730     def set_alpha(self, alpha):

/usr/local/lib/python3.7/site-packages/matplotlib/collections.py in _set_edgecolor(self, c)
    710         except AttributeError:
    711             pass
--> 712         self._edgecolors = mcolors.to_rgba_array(c, self._alpha)
    713         if set_hatch_color and len(self._edgecolors):
    714             self._hatch_color = tuple(self._edgecolors[0])

/usr/local/lib/python3.7/site-packages/matplotlib/colors.py in to_rgba_array(c, alpha)
    284     result = np.empty((len(c), 4), float)
    285     for i, cc in enumerate(c):
--> 286         result[i] = to_rgba(cc, alpha)
    287     return result
    288 

/usr/local/lib/python3.7/site-packages/matplotlib/colors.py in to_rgba(c, alpha)
    175         rgba = None
    176     if rgba is None:  # Suppress exception chaining of cache lookup failure.
--> 177         rgba = _to_rgba_no_colorcycle(c, alpha)
    178         try:
    179             _colors_full_map.cache[c, alpha] = rgba

/usr/local/lib/python3.7/site-packages/matplotlib/colors.py in _to_rgba_no_colorcycle(c, alpha)
    236         # float)` and `np.array(...).astype(float)` all convert "0.5" to 0.5.
    237         # Test dimensionality to reject single floats.
--> 238         raise ValueError("Invalid RGBA argument: {!r}".format(orig_c))
    239     # Return a tuple to prevent the cached value from being modified.
    240     c = tuple(c.astype(float))

ValueError: Invalid RGBA argument: masked

[mwaskom]

Looks like matplotlib 3.1 is breaking a lot of things. You’ll have to downgrade for the time being, sorry.

[stonebig]

the problem is solved in Matplolib master of today, for example by replacing the colors.py file entirely.

I think it's via this comit

https://github.com/matplotlib/matplotlib/commit/04baaf71b3f1242bfbc0dc12dc06c127878e558e

[mwaskom]

Great, thanks @stonebig.

[RylanSchaeffer]

What's the solution here? Wait for matplotlib to fix itself?

[MaozGelbart]

3.1.1 with the relevant bugfix has just been released.

[rpkarandev]

I am still problem in using catplot with poinplot and hue.
Matplotlib 3.1.1
Seaborn 0.9.0
Anaconda Python 3.6.7

The error I got is "ValueError: 'c' argument has 8 elements, which is not acceptable for use with 'x' with size 0, 'y' with size 0."

Please suggest some fix.

[liuq]

Same error here, in a similar situation.

[dmantadakis]

Same error for the above example while using the following configurations:

• Matplotlib='3.3.3' & Seaborn=0.11.1
• Matplotlib='3'3.2' & Seaborn=0.11.1

[mwaskom]

@dmantadakis it would be more helpful to provide a complete report but I think you're seeing a separate issue that's been reported to matplotlib here: https://github.com/matplotlib/matplotlib/issues/19066

[dmantadakis]

@mwaskom Here is the code

import pandas as pd
import seaborn as sns

df = sns.load_dataset("exercise")
df = df.drop(df.query("kind == 'walking' & time == '1 min'").index)
sns.catplot(x="time", y="pulse", hue="kind", kind='point', data=df)

and here is the Traceback

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-5-d161056f41d0> in <module>
      5 df = sns.load_dataset("exercise")
      6 df = df.drop(df.query("kind == 'walking' & time == '1 min'").index)
----> 7 sns.catplot(x="time", y="pulse", hue="kind", kind='point', data=df)

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/_decorators.py in inner_f(*args, **kwargs)
     44             )
     45         kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 46         return f(**kwargs)
     47     return inner_f
     48 

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/categorical.py in catplot(x, y, hue, data, row, col, col_wrap, estimator, ci, n_boot, units, seed, order, hue_order, row_order, col_order, kind, height, aspect, orient, color, palette, legend, legend_out, sharex, sharey, margin_titles, facet_kws, **kwargs)
   3842 
   3843     # Draw the plot onto the facets
-> 3844     g.map_dataframe(plot_func, x=x, y=y, hue=hue, **plot_kws)
   3845 
   3846     if p.orient == "h":

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/axisgrid.py in map_dataframe(self, func, *args, **kwargs)
    748 
    749             # Draw the plot
--> 750             self._facet_plot(func, ax, args, kwargs)
    751 
    752         # Finalize the annotations and layout

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/axisgrid.py in _facet_plot(self, func, ax, plot_args, plot_kwargs)
    773             plot_args = []
    774             plot_kwargs["ax"] = ax
--> 775         func(*plot_args, **plot_kwargs)
    776 
    777         # Sort out the supporting information

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/_decorators.py in inner_f(*args, **kwargs)
     44             )
     45         kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 46         return f(**kwargs)
     47     return inner_f
     48 

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/categorical.py in pointplot(x, y, hue, data, order, hue_order, estimator, ci, n_boot, units, seed, markers, linestyles, dodge, join, scale, orient, color, palette, errwidth, capsize, ax, **kwargs)
   3378         ax = plt.gca()
   3379 
-> 3380     plotter.plot(ax)
   3381     return ax
   3382 

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/categorical.py in plot(self, ax)
   1786     def plot(self, ax):
   1787         """Make the plot."""
-> 1788         self.draw_points(ax)
   1789         self.annotate_axes(ax)
   1790         if self.orient == "h":

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/seaborn/categorical.py in draw_points(self, ax)
   1779                     x = y = [np.nan] * n_points
   1780 
-> 1781                 ax.scatter(x, y, label=hue_level,
   1782                            facecolor=color, edgecolor=color,
   1783                            linewidth=mew, marker=marker, s=markersize,

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/__init__.py in inner(ax, data, *args, **kwargs)
   1445     def inner(ax, *args, data=None, **kwargs):
   1446         if data is None:
-> 1447             return func(ax, *map(sanitize_sequence, args), **kwargs)
   1448 
   1449         bound = new_sig.bind(ax, *args, **kwargs)

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/cbook/deprecation.py in wrapper(*inner_args, **inner_kwargs)
    409                          else deprecation_addendum,
    410                 **kwargs)
--> 411         return func(*inner_args, **inner_kwargs)
    412 
    413     return wrapper

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/axes/_axes.py in scatter(self, x, y, s, c, marker, cmap, norm, vmin, vmax, alpha, linewidths, verts, edgecolors, plotnonfinite, **kwargs)
   4486         offsets = np.ma.column_stack([x, y])
   4487 
-> 4488         collection = mcoll.PathCollection(
   4489                 (path,), scales,
   4490                 facecolors=colors,

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/collections.py in __init__(self, paths, sizes, **kwargs)
    951         """
    952 
--> 953         super().__init__(**kwargs)
    954         self.set_paths(paths)
    955         self.set_sizes(sizes)

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/cbook/deprecation.py in wrapper(*inner_args, **inner_kwargs)
    409                          else deprecation_addendum,
    410                 **kwargs)
--> 411         return func(*inner_args, **inner_kwargs)
    412 
    413     return wrapper

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/collections.py in __init__(self, edgecolors, facecolors, linewidths, linestyles, capstyle, joinstyle, antialiaseds, offsets, transOffset, norm, cmap, pickradius, hatch, urls, offset_position, zorder, **kwargs)
    173         self._hatch_color = mcolors.to_rgba(mpl.rcParams['hatch.color'])
    174         self.set_facecolor(facecolors)
--> 175         self.set_edgecolor(edgecolors)
    176         self.set_linewidth(linewidths)
    177         self.set_linestyle(linestyles)

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/collections.py in set_edgecolor(self, c)
    828         """
    829         self._original_edgecolor = c
--> 830         self._set_edgecolor(c)
    831 
    832     def set_alpha(self, alpha):

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/collections.py in _set_edgecolor(self, c)
    812         except AttributeError:
    813             pass
--> 814         self._edgecolors = mcolors.to_rgba_array(c, self._alpha)
    815         if set_hatch_color and len(self._edgecolors):
    816             self._hatch_color = tuple(self._edgecolors[0])

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/colors.py in to_rgba_array(c, alpha)
    339         return np.zeros((0, 4), float)
    340     else:
--> 341         return np.array([to_rgba(cc, alpha) for cc in c])
    342 
    343 

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/colors.py in <listcomp>(.0)
    339         return np.zeros((0, 4), float)
    340     else:
--> 341         return np.array([to_rgba(cc, alpha) for cc in c])
    342 
    343 

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/colors.py in to_rgba(c, alpha)
    187         rgba = None
    188     if rgba is None:  # Suppress exception chaining of cache lookup failure.
--> 189         rgba = _to_rgba_no_colorcycle(c, alpha)
    190         try:
    191             _colors_full_map.cache[c, alpha] = rgba

~/Sources/python_virtual_environments/.gslab_generic/lib/python3.8/site-packages/matplotlib/colors.py in _to_rgba_no_colorcycle(c, alpha)
    261     # tuple color.
    262     if not np.iterable(c):
--> 263         raise ValueError(f"Invalid RGBA argument: {orig_c!r}")
    264     if len(c) not in [3, 4]:
    265         raise ValueError("RGBA sequence should have length 3 or 4")

ValueError: Invalid RGBA argument: 0.4980392156862745