8000 NaN causes plt.vlines to not scale y limits · Issue #7406 · matplotlib/matplotlib · GitHub
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dadkins opened this issue Nov 4, 2016 · 2 comments · Fixed by #7408
Closed
2 tasks

NaN causes plt.vlines to not scale y limits #7406

dadkins opened this issue Nov 4, 2016 · 2 comments · Fixed by #7408
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@phobson
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status: confirmed bug
Milestone
v2.0.0

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@dadkins
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dadkins commented Nov 4, 2016 •
edited by dopplershift
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I have reduced the error to the following code snippet which I run in a Jupyter notebook. A NaN as the first item in the series causes plt.vlines to not scale the y limits appropriately. The data values are in the thousands, but the ylimits are [-0.06, 0.06].

%matplotlib inline
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import sys

print sys.version
print 'pandas', pd.__version__
print 'matplotlib', matplotlib.__version__
df = pd.DataFrame(index = pd.DatetimeIndex(['2016-10-07', '2016-10-14', '2016-10-21', '2016-10-28'], name='Date'),
                  data = [np.nan, -1000, -3000, 4500],
                  columns = ['Amount'])
print df

plt.figure(figsize=(12,3))
plt.vlines(df.index, 0, df['Amount'])
2.7.12 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:42:40) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
pandas 0.19.0
matplotlib 1.5.3
            Amount
Date              
2016-10-07     NaN
2016-10-14 -1000.0
2016-10-21 -3000.0
2016-10-28  4500.0

  • Matplotlib version, Python version and Platform (Windows, OSX, Linux ...)
    1.5.3, python 2.7.12, Linux

  • How did you install Matplotlib and Python (pip, anaconda, from source ...)
    conda

  • [ ]
    matplotlib-bug
@phobson
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phobson commented Nov 4, 2016

Thanks for the clear and detailed report. I can confirm this.

I can also confirm that moving to null value to a position other than the first in the sequence results in properly scaled axes.

An even more minimal example would be:

import matplotlib.pyplot as plt
import numpy as np
fig, ax = plt.subplots()
ax.vlines([1, 2, 3, 4], 0, [np.nan, -1000, -3000, 4500], colors='b', linewidth=5)

Of the top of my head, one way to fix this would be to check that the first element isn't null and remove it if it is. However, that feels like treating the symptom and not the cause.

Will need to dig further.

@phobson phobson added this to the 2.0.1 (next bug fix release) milestone Nov 4, 2016
@phobson phobson self-assigned this Nov 4, 2016
@tacaswell
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We are probably using np.min instead of np.nanmin and/or not masking the input properly.

phobson added a commit to phobson/matplotlib that referenced this issue Nov 4, 2016
@phobson
Use np.nanmin/max to determine limits in Axes.vlines
5ed9842 
Closes GH matplotlib#7406.
phobson added a commit to phobson/matplotlib that referenced this issue Nov 4, 2016
@phobson
Use np.nanmin/max to set ax limits in Axes.vlines
e0f560f 
Closes GH matplotlib#7406. Also applied fixes to Axes.hlines
and wrote tests for both.
@phobson phobson mentioned this issue Nov 4, 2016
Merged
phobson added a commit to phobson/matplotlib that referenced this issue Nov 7, 2016
@phobson
Use np.nanmin/max to set ax limits in Axes.vlines
747c3cd 
Closes GH matplotlib#7406. Also applied fixes to Axes.hlines
and wrote tests for both.
@QuLogic QuLogic modified the milestones: 2.0 (style change major release), 2.0.1 (next bug fix release) Dec 7, 2016
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Handle nan/masked values Axes.vlines and hlines phobson/matplotlib
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@tacaswell @QuLogic @dadkins @phobson
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