2/18/25, 6:48 PM Customizing Colorbars | Python Data Science Handbook

This is an excerpt from the Python Data Science Handbook (http://shop.oreilly.com/product/0636920034919.do) by Jake
VanderPlas; Jupyter notebooks are available on GitHub (https://github.com/jakevdp/PythonDataScienceHandbook).

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is released under the MIT license (https://opensource.org/licenses/MIT). If you find this content useful, please consider
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Customizing Colorbars

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Plot legends identify discrete labels of discrete points. For continuous labels
based on the color of points, lines, or regions, a labeled colorbar can be a great
tool. In Matplotlib, a colorbar is a separate axes that can provide a key for the
meaning of colors in a plot. Because the book is printed in black-and-white, this
section has an accompanying online supplement where you can view the
figures in full color (https://github.com/jakevdp/PythonDataScienceHandbook
(https://github.com/jakevdp/PythonDataScienceHandbook)). We'll start by
setting up the notebook for plotting and importing the functions we will use:

In [1]: import matplotlib.pyplot as plt

plt.style.use('classic')

In [2]: %matplotlib inline

import numpy as np

As we have seen several times throughout this section, the simplest colorbar
can be created with the plt.colorbar function:

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In [3]: x = np.linspace(0, 10, 1000)

I = np.sin(x) * np.cos(x[:, np.newaxis])

plt.imshow(I)
plt.colorbar();

We'll now discuss a few ideas for customizing these colorbars and using them
effectively in various situations.

# Customizing Colorbars
The colormap can be specified using the cmap argument to the plotting
function that is creating the visualization:

In [4]: plt.imshow(I, cmap='gray');

All the available colormaps are in the plt.cm namespace; using IPython's tab-
completion will give you a full list of built-in possibilities:

plt.cm.<TAB>

But being able to choose a colormap is just the first step: more important is
how to decide among the possibilities! The choice turns out to be much more
subtle than you might initially expect.

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2/18/25, 6:48 PM Customizing Colorbars | Python Data Science Handbook

## Choosing the Colormap

A full treatment of color choice within visualization is beyond the scope of this
book, but for entertaining reading on this subject and others, see the article
"Ten Simple Rules for Better Figures"
(http://journals.plos.org/ploscompbiol/article?
id=10.1371/journal.pcbi.1003833). Matplotlib's online documentation also has
an interesting discussion (http://Matplotlib.org/1.4.1/users/colormaps.html) of
colormap choice.

Broadly, you should be aware of three different categories of colormaps:

Sequential colormaps: These are made up of one continuous sequence of

colors (e.g., binary or viridis ).
Divergent colormaps: These usually contain two distinct colors, which
show positive and negative deviations from a mean (e.g., RdBu or PuOr ).
Qualitative colormaps: these mix colors with no particular sequence (e.g.,
rainbow or jet ).

The jet colormap, which was the default in Matplotlib prior to version 2.0, is
an example of a qualitative colormap. Its status as the default was quite
unfortunate, because qualitative maps are often a poor choice for representing
quantitative data. Among the problems is the fact that qualitative maps usually
do not display any uniform progression in brightness as the scale increases.

We can see this by converting the jet colorbar into black and white:

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In [5]: from matplotlib.colors import LinearSegmentedColormap

def grayscale_cmap(cmap):
"""Return a grayscale version of the given colormap"""
cmap = plt.cm.get_cmap(cmap)
colors = cmap(np.arange(cmap.N))

# convert RGBA to perceived grayscale luminance

# cf. http://alienryderflex.com/hsp.html
RGB_weight = [0.299, 0.587, 0.114]
luminance = np.sqrt(np.dot(colors[:, :3] ** 2, RGB_weight))
colors[:, :3] = luminance[:, np.newaxis]

return LinearSegmentedColormap.from_list(cmap.name + "_gray", co

def view_colormap(cmap):
"""Plot a colormap with its grayscale equivalent"""
cmap = plt.cm.get_cmap(cmap)
colors = cmap(np.arange(cmap.N))

cmap = grayscale_cmap(cmap)
grayscale = cmap(np.arange(cmap.N))

fig, ax = plt.subplots(2, figsize=(6, 2),

subplot_kw=dict(xticks=[], yticks=[]))
ax[0].imshow([colors], extent=[0, 10, 0, 1])
ax[1].imshow([grayscale], extent=[0, 10, 0, 1])

In [6]: view_colormap('jet')

Notice the bright stripes in the grayscale image. Even in full color, this uneven
brightness means that the eye will be drawn to certain portions of the color
range, which will potentially emphasize unimportant parts of the dataset. It's
better to use a colormap such as viridis (the default as of Matplotlib 2.0),
which is specifically constructed to have an even brightness variation across the
range. Thus it not only plays well with our color perception, but also will
translate well to grayscale printing:

In [7]: view_colormap('viridis')

If you favor rainbow schemes, another good option for continuous data is the
cubehelix colormap:

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In [8]: view_colormap('cubehelix')

For other situations, such as showing positive and negative deviations from
some mean, dual-color colorbars such as RdBu (Red-Blue) can be useful.
However, as you can see in the following figure, it's important to note that the
positive-negative information will be lost upon translation to grayscale!

In [9]: view_colormap('RdBu')

We'll see examples of using some of these color maps as we continue.

There are a large number of colormaps available in Matplotlib; to see a list of

them, you can use IPython to explore the plt.cm submodule. For a more
principled approach to colors in Python, you can refer to the tools and
documentation within the Seaborn library (see Visualization With Seaborn
(04.14-visualization-with-seaborn.html)).

## Color limits and extensions

Matplotlib allows for a large range of colorbar customization. The colorbar itself
is simply an instance of plt.Axes , so all of the axes and tick formatting tricks
we've learned are applicable. The colorbar has some interesting flexibility: for
example, we can narrow the color limits and indicate the out-of-bounds values
with a triangular arrow at the top and bottom by setting the extend property.
This might come in handy, for example, if displaying an image that is subject to
noise:

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In [10]: # make noise in 1% of the image pixels

speckles = (np.random.random(I.shape) < 0.01)
I[speckles] = np.random.normal(0, 3, np.count_nonzero(speckles))

plt.figure(figsize=(10, 3.5))

plt.subplot(1, 2, 1)
plt.imshow(I, cmap='RdBu')
plt.colorbar()

plt.subplot(1, 2, 2)
plt.imshow(I, cmap='RdBu')
plt.colorbar(extend='both')
plt.clim(-1, 1);

Notice that in the left panel, the default color limits respond to the noisy pixels,
and the range of the noise completely washes-out the pattern we are interested
in. In the right panel, we manually set the color limits, and add extensions to
indicate values which are above or below those limits. The result is a much
more useful visualization of our data.

## Discrete Color Bars

Colormaps are by default continuous, but sometimes you'd like to represent
discrete values. The easiest way to do this is to use the plt.cm.get_cmap()
function, and pass the name of a suitable colormap along with the number of
desired bins:

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In [11]: plt.imshow(I, cmap=plt.cm.get_cmap('Blues', 6))

plt.colorbar()
plt.clim(-1, 1);

The discrete version of a colormap can be used just like any other colormap.

# Example: Handwritten Digits

For an example of where this might be useful, let's look at an interesting
visualization of some hand written digits data. This data is included in Scikit-
Learn, and consists of nearly 2,000 8 × 8 thumbnails showing various hand-
written digits.

For now, let's start by downloading the digits data and visualizing several of the
example images with plt.imshow() :

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In [12]: # load images of the digits 0 through 5 and visualize several of the
from sklearn.datasets import load_digits
digits = load_digits(n_class=6)

fig, ax = plt.subplots(8, 8, figsize=(6, 6))

for i, axi in enumerate(ax.flat):
axi.imshow(digits.images[i], cmap='binary')
axi.set(xticks=[], yticks=[])

Because each digit is defined by the hue of its 64 pixels, we can consider each
digit to be a point lying in 64-dimensional space: each dimension represents the
brightness of one pixel. But visualizing relationships in such high-dimensional
spaces can be extremely difficult. One way to approach this is to use a
dimensionality reduction technique such as manifold learning to reduce the
dimensionality of the data while maintaining the relationships of interest.
Dimensionality reduction is an example of unsupervised machine learning, and
we will discuss it in more detail in What Is Machine Learning? (05.01-what-is-
machine-learning.html).

Deferring the discussion of these details, let's take a look at a two-dimensional

manifold learning projection of this digits data (see In-Depth: Manifold Learning
(05.10-manifold-learning.html) for details):

In [13]: # project the digits into 2 dimensions using IsoMap

from sklearn.manifold import Isomap
iso = Isomap(n_components=2)
projection = iso.fit_transform(digits.data)

We'll use our discrete colormap to view the results, setting the ticks and
clim to improve the aesthetics of the resulting colorbar:

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In [14]: # plot the results

plt.scatter(projection[:, 0], projection[:, 1], lw=0.1,
c=digits.target, cmap=plt.cm.get_cmap('cubehelix', 6))
plt.colorbar(ticks=range(6), label='digit value')
plt.clim(-0.5, 5.5)

The projection also gives us some interesting insights on the relationships

within the dataset: for example, the ranges of 5 and 3 nearly overlap in this
projection, indicating that some hand written fives and threes are difficult to
distinguish, and therefore more likely to be confused by an automated
classification algorithm. Other values, like 0 and 1, are more distantly
separated, and therefore much less likely to be confused. This observation
agrees with our intuition, because 5 and 3 look much more similar than do 0
and 1.

We'll return to manifold learning and to digit classification in Chapter 5 (05.00-

machine-learning.html).

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