How to create a 2d histogram with matplotlib ?

Examples of how to create a 2d histogram with matplotlib

Using the matplotlib hist2d function

To create a 2d histogram in python there are several solutions: for example there is the matplotlib function hist2d.

from numpy import c_

import numpy as np
import matplotlib.pyplot as plt
import random

n = 100000

x = np.random.standard_normal(n)
y = 3.0 * x + 2.0 * np.random.standard_normal(n)

Note: if the data are stored in a file (called data.txt for example):

-1.97965874896 -7.16247661299
-0.326184108313 -3.30336677657
0.804581568977 2.01236810129
0.956767993891 5.73449356815
0.640996608682 4.80528729039
0.516617563432 1.89773430157
-0.263865123489 -0.708296452938
-0.282288527909 -0.938531482069
2.40868958562 10.4996832992
-1.9819139465 -7.84691502438
.
.
.

there is the numpy function loadtxt():

x, y = np.loadtxt("data.txt",unpack=True)

Plot the 2d histogram:

plt.hist2d(x,y)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_01.png", bbox_inches='tight')

plt.close()

Get histogram parameters

It is possible to get the histogram parameters:

h, xedges, yedges, image = plt.hist2d(x,y)

print(h)
print('----------')

print(xedges)
print('----------')

print(yedges)
print('----------')

plt.close()

Change the bins size

The option bin can be used ti change the bins size:

plt.hist2d(x,y,bins=50)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_02.png", bbox_inches='tight')

plt.close()

Another example:

x_min = np.min(x)
x_max = np.max(x)

y_min = np.min(y)
y_max = np.max(y)

x_bins = np.linspace(x_min,x_max,50)
y_bins = np.linspace(y_min,y_max,20)

plt.hist2d(x,y,bins=[x_bins,y_bins])

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_03.png", bbox_inches='tight')

plt.close()

Change color scale

The option cmap can be used to change the color scale (see Choosing Colormaps in Matplotlib)

plt.hist2d(x,y,bins=50, cmap=plt.cm.jet)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_04.png", bbox_inches='tight')

plt.close()

Add a color bar

Add the line plt.colorbar() to create a color bar

plt.hist2d(x,y,bins=50, cmap=plt.cm.jet)

plt.colorbar()

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_08.png", bbox_inches='tight')

plt.close()

Filter the data

Another example:

data = c_[x,y]

for i in range(100):
    x_idx = random.randint(0,n-1)
    data[x_idx,0] = -999

data = data[data[:,0]!=-999]

plt.hist2d(data[:,0],data[:,1],bins=50, cmap=plt.cm.jet)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_05.png", bbox_inches='tight')

plt.close()

Using the matplotlib hexbin function

Another solution using the matplotlib function hexbin:

plt.hexbin(x,y,bins=50, cmap=plt.cm.jet)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_06.png", bbox_inches='tight')

plt.close()

Using the numpy histogram2d function

Another solution the numpy function histogram2d

heatmap, xedges, yedges = np.histogram2d(x, y, bins=50)
#extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]

plt.imshow(heatmap,origin='lower')
#plt.imshow(heatmap,origin='lower', extent=extent)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_07.png", bbox_inches='tight')

plt.close()

Example of python code

from numpy import c_

import numpy as np
import matplotlib.pyplot as plt
import random

n = 100000

x = np.random.standard_normal(n)
y = 3.0 * x + 2.0 * np.random.standard_normal(n)

# read data from a file:

#x, y = np.loadtxt("data.txt",unpack=True)

#for i in range(10):
#   print(x[i],y[i])

#----------------------------------------------------------------------------------------#
# Using matplotlib hist2d function

plt.hist2d(x,y)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_01.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Get 2d histogram model paramaters

h, xedges, yedges, image = plt.hist2d(x,y)

print(h)
print('----------')

print(xedges)
print('----------')

print(yedges)
print('----------')

plt.close()

#----------------------------------------------------------------------------------------#
# Change bins size

plt.hist2d(x,y,bins=50)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_02.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Change bins size (custume size)

x_min = np.min(x)
x_max = np.max(x)

y_min = np.min(y)
y_max = np.max(y)

x_bins = np.linspace(x_min,x_max,50)
y_bins = np.linspace(y_min,y_max,20)

plt.hist2d(x,y,bins=[x_bins,y_bins])

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_03.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Change the color bar

plt.hist2d(x,y,bins=50, cmap=plt.cm.jet)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_04.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Add color bar

plt.hist2d(x,y,bins=50, cmap=plt.cm.jet)

plt.colorbar()

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_08.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Filter the data

data = c_[x,y]

for i in range(100):
    x_idx = random.randint(0,n-1)
    data[x_idx,0] = -999

data = data[data[:,0]!=-999]

plt.hist2d(data[:,0],data[:,1],bins=50, cmap=plt.cm.jet)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_05.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Using matplotlib hexbin function

plt.hexbin(x,y,bins=50, cmap=plt.cm.jet)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_06.png", bbox_inches='tight')

plt.close()

#----------------------------------------------------------------------------------------#
# Using numpy hexbin function

heatmap, xedges, yedges = np.histogram2d(x, y, bins=50)
#extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]

plt.imshow(heatmap,origin='lower')
#plt.imshow(heatmap,origin='lower', extent=extent)

plt.title("How to plot a 2d histogram with matplotlib ?")

plt.savefig("histogram_2d_07.png", bbox_inches='tight')

plt.close()

References