matplotlib plot data with nans

Question

I'm surprised how few are the posts relating to this problem. Anyway... here it is: I have csv data files containing X values in the first column, and several Y values columns thereafter. But for a given X value not all Y series have a corresponding value. Here is an example:

0, 16, 96, 99
10, 88, 45, 85
20, 85, 61, 10
30, 30, --, 45
40, 82, 28, 82
50, 23, 9, 61
60, 40, 77, 0
70, 26, 21, --
80, --, 58, 99
90, 1, 14, 30

when this csv data is loaded with numpy.genfromtxt, the '--' strings are taken as nan which is good. But when plotting, the plots are interrupted with blanks where there is a nan. Is there an option when a nan appears to make pyplot.plot() ignoring both the nan and the corresponding X value?

Jaime · Accepted Answer · 2013-01-23 10:32:07Z

3

Not sure if matplotlib has such functionality built in, but you could home-brew it doing the following:

idx = ~numpy.isnan(Y)
pyplot.plot(X[idx], Y[idx])

answered Jan 23, 2013 at 10:32

Jaime

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Community · Accepted Answer · 2017-05-23 12:12:16Z

2

Look at this post

As proposed in my answer there, I'd recommend using np.isfinite instead of np.isnan. There might be other reasons for your plot to have discontinuities, e.f., inf

edited May 23, 2017 at 12:12

CommunityBot

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answered Jan 23, 2013 at 10:35

Thorsten Kranz

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1 Comment

user1850133 Over a year ago

ok, from what I saw in the post you linked here, this one can be marked as duplicate as that one. Anyway, thanks for your solution.

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