LinAlgError: singular matrix with data having all mass at 0 for some steps

[macks22]

I get a LinAlgError: singular matrix when attempting to plot a joyplot on data that has groups with all zeros (i.e. all mass at exactly 0). It seems this is an issue from the direct pass-through to the kde estimator and ultimately comes from trying to take the inverse of a singular covariance matrix. While one could argue that is reasonable expected behavior, I feel a better default in this situation would be to plot a vertical line at x = 0, y = 1 (no tails). You can reproduce the described error via:

from joypy import joyplot
df = pd.DataFrame({
    'value': np.concatenate([np.random.uniform(0, 1, size=100), np.random.uniform(0.5, 1, size=100), np.zeros(100)]),
    'time': np.concatenate([np.zeros(100), np.ones(100), np.ones(100) * 2]).astype(int)
})
joyplot(df, by='time', columns=['value'])

Versions:

python==3.6.1
joypy==0.1.7
scipy==1.0.0
numpy==1.13.3
matplotlib=2.1.1

The exact error message is:

---------------------------------------------------------------------------
LinAlgError                               Traceback (most recent call last)
<ipython-input-14-35fa7743dda5> in <module>()
----> 1 joyplot(df, by='time', columns=['value'])

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/joypy/joyplot.py in joyplot(data, column, by, grid, xlabelsize, xrot, ylabelsize, yrot, ax, figsize, hist, bins, fade, ylim, fill, linecolor, overlap, background, labels, xlabels, ylabels, range_style, x_range, title, colormap, **kwds)
    233                     title=title,
    234                     colormap=colormap,
--> 235                     **kwds)
    236
    237 ###########################################

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/joypy/joyplot.py in _joyplot(data, grid, labels, sublabels, xlabels, xlabelsize, xrot, ylabelsize, yrot, ax, figsize, hist, bins, fade, xlim, ylim, fill, linecolor, overlap, background, range_style, x_range, tails, title, legend, loc, colormap, color, **kwargs)
    437                              fill=fill, linecolor=linecolor, label=sublabel,
    438                              zorder=element_zorder, color=element_color,
--> 439                              bins=bins, **kwargs)
    440
    441

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/joypy/joyplot.py in plot_density(ax, x_range, v, kind, bw_method, bins, fill, linecolor, clip_on, **kwargs)
    248
    249     if kind == "kde":
--> 250         gkde = gaussian_kde(v, bw_method=bw_method)
    251         y = gkde.evaluate(x_range)
    252     elif kind == "counts":

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/scipy/stats/kde.py in __init__(self, dataset, bw_method)
    170
    171         self.d, self.n = self.dataset.shape
--> 172         self.set_bandwidth(bw_method=bw_method)
    173
    174     def evaluate(self, points):

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/scipy/stats/kde.py in set_bandwidth(self, bw_method)
    497             raise ValueError(msg)
    498
--> 499         self._compute_covariance()
    500
    501     def _compute_covariance(self):

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/scipy/stats/kde.py in _compute_covariance(self)
    508             self._data_covariance = atleast_2d(np.cov(self.dataset, rowvar=1,
    509                                                bias=False))
--> 510             self._data_inv_cov = linalg.inv(self._data_covariance)
    511
    512         self.covariance = self._data_covariance * self.factor**2

/Users/mack/anaconda2/envs/py3k/lib/python3.6/site-packages/scipy/linalg/basic.py in inv(a, overwrite_a, check_finite)
    974         inv_a, info = getri(lu, piv, lwork=lwork, overwrite_lu=1)
    975     if info > 0:
--> 976         raise LinAlgError("singular matrix")
    977     if info < 0:
    978         raise ValueError('illegal value in %d-th argument of internal '

LinAlgError: singular matrix

[leotac]

I feel a better default in this situation would be to plot a vertical line at x = 0, y = 1 (no tails).

Sounds reasonable. Feel free to open a PR if you want.

[albacrespi]

I have the same problem. I added some noise to my matrix but still gives the same error. What can I try to plot by groups?