matplotlib: plotting histogram plot just above scatter plot

Question

I would like to make beautiful scatter plots with histograms above and right of the scatter plot, as it is possible in seaborn with jointplot:

I am looking for suggestions on how to achieve this. In fact I am having some troubles in installing pandas, and also I do not need the entire seaborn module

To be clear, your question is how to implement sns.jointplot in vanilla matplotlib? — wflynny
– wflynny, Commented May 3, 2016 at 15:32
more or less. my question is how to place another box above a scatter plot, so I can draw an histogram there — simona
– simona, Commented May 3, 2016 at 15:34
Check out matplotlib.gridspec.GridSpec, specifically the example at the bottom. Without gridspec, you can follow this clear example — wflynny
– wflynny, Commented May 3, 2016 at 15:36
Further, here's a similar example on stackoverflow: stackoverflow.com/questions/20525983/… — wflynny
– wflynny, Commented May 3, 2016 at 15:38
Matplotlib now has an own example on 'Show the marginal distributions of a scatter plot as histograms at the sides of the plot.': matplotlib.org/stable/gallery/axes_grid1/… — Jaleks
– Jaleks, Commented Oct 18, 2023 at 17:59

BiGYaN · Accepted Answer · 2021-01-18 18:03:33Z

27

I encountered the same problem today. Additionally I wanted a CDF for the marginals.

Code:

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

x = np.random.beta(2,5,size=int(1e4))
y = np.random.randn(int(1e4))

fig = plt.figure(figsize=(8,8))
gs = gridspec.GridSpec(3, 3)
ax_main = plt.subplot(gs[1:3, :2])
ax_xDist = plt.subplot(gs[0, :2],sharex=ax_main)
ax_yDist = plt.subplot(gs[1:3, 2],sharey=ax_main)
    
ax_main.scatter(x,y,marker='.')
ax_main.set(xlabel="x data", ylabel="y data")

ax_xDist.hist(x,bins=100,align='mid')
ax_xDist.set(ylabel='count')
ax_xCumDist = ax_xDist.twinx()
ax_xCumDist.hist(x,bins=100,cumulative=True,histtype='step',density=True,color='r',align='mid')
ax_xCumDist.tick_params('y', colors='r')
ax_xCumDist.set_ylabel('cumulative',color='r')

ax_yDist.hist(y,bins=100,orientation='horizontal',align='mid')
ax_yDist.set(xlabel='count')
ax_yCumDist = ax_yDist.twiny()
ax_yCumDist.hist(y,bins=100,cumulative=True,histtype='step',density=True,color='r',align='mid',orientation='horizontal')
ax_yCumDist.tick_params('x', colors='r')
ax_yCumDist.set_xlabel('cumulative',color='r')

plt.show()

Hope it helps the next person searching for scatter-plot with marginal distribution.

edited Jan 18, 2021 at 18:03

answered Mar 24, 2018 at 20:12

BiGYaN

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2 Comments

Leo Over a year ago

Your pic is beautiful, +1, but the code returns an error: AttributeError: 'Polygon' object has no property 'normed'. Please correct your solution or tell me what I'm doing wrong.

Leo Over a year ago

Figured it out: replace normed=True with density=True.

tmdavison · Accepted Answer · 2016-05-03 16:55:04Z

13

Here's an example of how to do it, using gridspec.GridSpec:

import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import numpy as np

x = np.random.rand(50)
y = np.random.rand(50)

fig = plt.figure()

gs = GridSpec(4,4)

ax_joint = fig.add_subplot(gs[1:4,0:3])
ax_marg_x = fig.add_subplot(gs[0,0:3])
ax_marg_y = fig.add_subplot(gs[1:4,3])

ax_joint.scatter(x,y)
ax_marg_x.hist(x)
ax_marg_y.hist(y,orientation="horizontal")

# Turn off tick labels on marginals
plt.setp(ax_marg_x.get_xticklabels(), visible=False)
plt.setp(ax_marg_y.get_yticklabels(), visible=False)

# Set labels on joint
ax_joint.set_xlabel('Joint x label')
ax_joint.set_ylabel('Joint y label')

# Set labels on marginals
ax_marg_y.set_xlabel('Marginal x label')
ax_marg_x.set_ylabel('Marginal y label')
plt.show()

edited May 3, 2016 at 16:55

answered May 3, 2016 at 15:46

tmdavison

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3 Comments

simona Over a year ago

nice, but how do I remove ticks only from the histograms (without suppressing axes), and how do I add labels selectively?

tmdavison Over a year ago

See here stackoverflow.com/questions/4209467/…

simona Over a year ago

now my labels appear on the plot [0,0] instead than [1,0]. I want ylabel on plot [0,0], xlabel on plot[1,1], and both labels on plot [1,0]

Carlos Pinzón · Accepted Answer · 2022-01-07 02:59:15Z

4

I strongly recommend to flip the right histogram by adding these 3 lines of code to the current best answer before plt.show() :

ax_yDist.invert_xaxis()
ax_yDist.yaxis.tick_right()
ax_yCumDist.invert_xaxis()

The advantage is that any person who is visualizing it can compare easily the two histograms just by moving and rotating clockwise the right histogram on their mind.

On contrast, in the plot of the question and in all other answers, if you want to compare the two histograms, your first reaction is to rotate the right histogram counterclockwise, which leads to wrong conclusions because the y axis gets inverted. Indeed, the right CDF of the current best answer looks decreasing at first sight:

edited Jan 7, 2022 at 2:59

answered Dec 1, 2021 at 11:45

Carlos Pinzón

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