Density Plot with Matplotlib


This post aims to display density plots built with matplotlib and shows how to calculate a 2D kernel density estimate.

Let’s consider that you want to study the relationship between 2 numerical variables with a lot of points. Then you can consider the number of points on each part of the plotting area and thus calculate a 2D kernel density estimate. It is like a smoothed histogram. Instead of a point falling into a particular bin, it adds a weight to surrounding bins. This plot is inspired from this stack overflow question. See this page to custom the color palette.

# libraries
import matplotlib.pyplot as plt
import numpy as np
from scipy.stats import kde
 
# create data
x = np.random.normal(size=500)
y = x * 3 + np.random.normal(size=500)
 
# Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
nbins=300
k = kde.gaussian_kde([x,y])
xi, yi = np.mgrid[x.min():x.max():nbins*1j, y.min():y.max():nbins*1j]
zi = k(np.vstack([xi.flatten(), yi.flatten()]))
 
# Make the plot
plt.pcolormesh(xi, yi, zi.reshape(xi.shape), shading='auto')
plt.show()
 
# Change color palette
plt.pcolormesh(xi, yi, zi.reshape(xi.shape), shading='auto', cmap=plt.cm.Greens_r)
plt.show()

You can add a color bar easily using colorbar() function.

# Add color bar
plt.pcolormesh(xi, yi, zi.reshape(xi.shape), shading='auto', cmap=plt.cm.Greens_r)
plt.colorbar()
plt.show()

Scatterplot

Heatmap

Correlogram

Bubble

Connected Scatter

2D Density

Contact & Edit

πŸ‘‹ This document is a work by Yan Holtz. Any feedback is highly encouraged. You can fill an issue on Github, drop me a message onTwitter, or send an email pasting yan.holtz.data with gmail.com.

This page is just a jupyter notebook, you can edit it here. Please help me making this website better πŸ™!

Violin

Density

Histogram

Boxplot

Ridgeline

Scatterplot

Heatmap

Correlogram

Bubble

Connected Scatter

2D Density

Barplot

Spider / Radar

Wordcloud

Parallel

Lollipop

Circular Barplot

Treemap

Venn Diagram

Donut

Pie Chart

Dendrogram

Circular Packing

Line chart

Area chart

Stacked Area

Streamgraph

Map

Choropleth

Hexbin

Cartogram

Connection

Bubble

Chord Diagram

Network

Sankey

Arc Diagram

Edge Bundling

Colors

Interactivity

Animation with python

Animation

Cheat sheets

Caveats

3D