how to add error bars to histogram diagram in python

Question

Hi I want to add error bars to the histogram within this code.I have seen few post about it but I didn't find them helpful.this code produce random numbers with Gaussian distribution and a kernel estimation apply to it.I need to have errorbars to estimate how much the histogram is inaccurate with changing the bandwidth

from random import * 
import numpy as np 
from matplotlib.pyplot import* 
from matplotlib import* 
import scipy.stats as stats

def hist_with_kde(data, bandwidth = 0.3):
    #set number of bins using Freedman and Diaconis
    q1 = np.percentile(data,25)
    q3 = np.percentile(data,75)


    n = len(data)**(.1/.3)
    rng = max(data) - min(data)
    iqr = 2*(q3-q1)

    bins =int((n*rng)/iqr)
    print(bins)
    x = np.linspace(min(data),max(data),200)

    kde = stats.gaussian_kde(data,'scott')

    kde._compute_covariance()
    kde.set_bandwidth()


    plot(x,kde(x),'r') # distribution function
    hist(data,bins=bins,normed=True) # histogram

data = np.random.normal(0,1,1000)
hist_with_kde(data,30)

show()

I get errors, if I execute your code (in line 30: date = ...) — bastelflp, Feb 14 '16 at 09:35
You are missing an ";" or a newline in line 30, like so: `data = np.random.normal(0,1,1000); hist_with_kde(data,30)` — Mikkel Bue Tellus, Feb 14 '16 at 09:36
Possible duplicate of [Matplotlib histogram with errorbars](http://stackoverflow.com/questions/11774822/matplotlib-histogram-with-errorbars) — bastelflp, Feb 14 '16 at 09:45

score 2 · Accepted Answer · edited May 23 '17 at 11:45

Combining the answer mentioned above with your code:

import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as stats


def hist_with_kde(data, bandwidth = 0.3):
    #set number of bins using Freedman and Diaconis
    q1 = np.percentile(data, 25)
    q3 = np.percentile(data, 75)

    n = len(data)**(.1/.3)
    rng = max(data) - min(data)
    iqr = 2*(q3-q1)

    bins =int((n*rng)/iqr)
    print(bins)
    x = np.linspace(min(data), max(data), 200)

    kde = stats.gaussian_kde(data, 'scott')

    kde._compute_covariance()
    kde.set_bandwidth()

    plt.plot(x, kde(x), 'r')  # distribution function

    y, binEdges = np.histogram(data, bins=bins, normed=True)
    bincenters = 0.5*(binEdges[1:]+binEdges[:-1])
    menStd = np.sqrt(y)
    width = 0.2
    plt.bar(bincenters, y, width=width, color='r', yerr=menStd)


data = np.random.normal(0, 1, 1000)
hist_with_kde(data, 30)

plt.show()

And have a look at the imports, as mentioned by MaxNoe

thank you for such a quick help.I only have one trouble.why can't I see my kernel density distribution in your code?I prefer to have both errors and kernel distribution — jack, Feb 14 '16 at 10:10
I updated the code and put the error bars inside the kde function as mentioned by [Mikkel Bue Tellus](http://stackoverflow.com/a/35390334/5276734) but now you have a normed hist, but the error bars are not normed - so the plot does not match. — bastelflp, Feb 14 '16 at 10:49

score 2 · Answer 2 · answered Feb 14 '16 at 10:00

You can do it like this:

import numpy as np
import matplotlib.pyplot as plt

plt.style.use('ggplot')

data = np.random.normal(size=10000)

# plt.hist gives you the entries, edges 
# and drawables we do not need the drawables:
entries, edges, _ = plt.hist(data, bins=25, range=[-5, 5])

# calculate bin centers
bin_centers = 0.5 * (edges[:-1] + edges[1:])

# draw errobars, use the sqrt error. You can use what you want there
# poissonian 1 sigma intervals would make more sense
plt.errorbar(bin_centers, entries, yerr=np.sqrt(entries), fmt='r.')

plt.show()

Result:

score 0 · Answer 3 · edited May 23 '17 at 12:15

0

This looks like a duplicate: Matplotlib histogram with errorbars

i.e. you have to use matplotlib.bar() to get error bars

Which in your example will look something like this: You can replace

hist(data,bins=bins,normed=True)

with

y, binEdges = np.histogram(data,bins=bins)
bincenters = 0.5*(binEdges[1:]+binEdges[:-1])
menStd = np.sqrt(y)
width=0.1
bar(bincenters,y,width=width, color='r', yerr=menStd)

Play around with the parameters until you find something you like :)

edited May 23 '17 at 12:15

Community

1
1

answered Feb 14 '16 at 09:40

Mikkel Bue Tellus

73
1
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I've read that but I can't apply that to my code.I'm quite beginner to plot in python – jack Feb 14 '16 at 09:49
*Moved to answer section* – Mikkel Bue Tellus Feb 14 '16 at 09:58

how to add error bars to histogram diagram in python

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