Simple Scatter Plots

Another commonly used plot type is the simple scatter plot, a close cousin of the line
plot. Instead of points being joined by line segments, here the points are represented
individually with a dot, circle, or other shape. We’ll start by setting up the notebook
for plotting and importing the functions we will use:
In[1]: %matplotlib inline
import matplotlib.pyplot as plt
plt.style.use('seaborn-whitegrid')
import numpy as np

Scatter Plots with plt.plot

In the previous section, we looked at plt.plot/ax.plot to produce line plots. It turns
out that this same function can produce scatter plots as well (Figure 4-20):
In[2]: x = np.linspace(0, 10, 30)
y = np.sin(x)

plt.plot(x, y, 'o', color='black');

Figure 4-20. Scatter plot example

The third argument in the function call is a character that represents the type of sym‐
bol used for the plotting. Just as you can specify options such as '-' and '--' to con‐
trol the line style, the marker style has its own set of short string codes. The full list of
available symbols can be seen in the documentation of plt.plot, or in Matplotlib’s
online documentation. Most of the possibilities are fairly intuitive, and we’ll show a
number of the more common ones here (Figure 4-21):
In[3]: rng = np.random.RandomState(0)
for marker in ['o', '.', ',', 'x', '+', 'v', '^', '<', '>', 's', 'd']:
plt.plot(rng.rand(5), rng.rand(5), marker,
label="marker='{0}'".format(marker))

Simple Scatter Plots | 233

 plt.legend(numpoints=1)
plt.xlim(0, 1.8);

Figure 4-21. Demonstration of point numbers

For even more possibilities, these character codes can be used together with line and
color codes to plot points along with a line connecting them (Figure 4-22):
In[4]: plt.plot(x, y, '-ok'); # line (-), circle marker (o), black (k)

Figure 4-22. Combining line and point markers

Additional keyword arguments to plt.plot specify a wide range of properties of the

lines and markers (Figure 4-23):
In[5]: plt.plot(x, y, '-p', color='gray',
markersize=15, linewidth=4,
markerfacecolor='white',
markeredgecolor='gray',
markeredgewidth=2)
plt.ylim(-1.2, 1.2);

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Figure 4-23. Customizing line and point numbers

This type of flexibility in the plt.plot function allows for a wide variety of possible
visualization options. For a full description of the options available, refer to the
plt.plot documentation.

Scatter Plots with plt.scatter

A second, more powerful method of creating scatter plots is the plt.scatter func‐
tion, which can be used very similarly to the plt.plot function (Figure 4-24):
In[6]: plt.scatter(x, y, marker='o');

Figure 4-24. A simple scatter plot

The primary difference of plt.scatter from plt.plot is that it can be used to create
scatter plots where the properties of each individual point (size, face color, edge color,
etc.) can be individually controlled or mapped to data.
Let’s show this by creating a random scatter plot with points of many colors and sizes.
In order to better see the overlapping results, we’ll also use the alpha keyword to
adjust the transparency level (Figure 4-25):

Simple Scatter Plots | 235

 In[7]: rng = np.random.RandomState(0)
x = rng.randn(100)
y = rng.randn(100)
colors = rng.rand(100)
sizes = 1000 * rng.rand(100)

plt.scatter(x, y, c=colors, s=sizes, alpha=0.3,

cmap='viridis')
plt.colorbar(); # show color scale

Figure 4-25. Changing size, color, and transparency in scatter points

Notice that the color argument is automatically mapped to a color scale (shown here
by the colorbar() command), and the size argument is given in pixels. In this way,
the color and size of points can be used to convey information in the visualization, in
order to illustrate multidimensional data.
For example, we might use the Iris data from Scikit-Learn, where each sample is one
of three types of flowers that has had the size of its petals and sepals carefully meas‐
ured (Figure 4-26):
In[8]: from sklearn.datasets import load_iris
iris = load_iris()
features = iris.data.T

plt.scatter(features[0], features[1], alpha=0.2,

s=100*features[3], c=iris.target, cmap='viridis')
plt.xlabel(iris.feature_names[0])
plt.ylabel(iris.feature_names[1]);

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Figure 4-26. Using point properties to encode features of the Iris data

We can see that this scatter plot has given us the ability to simultaneously explore
four different dimensions of the data: the (x, y) location of each point corresponds to
the sepal length and width, the size of the point is related to the petal width, and the
color is related to the particular species of flower. Multicolor and multifeature scatter
plots like this can be useful for both exploration and presentation of data.

plot Versus scatter: A Note on Efficiency

Aside from the different features available in plt.plot and plt.scatter, why might
you choose to use one over the other? While it doesn’t matter as much for small
amounts of data, as datasets get larger than a few thousand points, plt.plot can be
noticeably more efficient than plt.scatter. The reason is that plt.scatter has the
capability to render a different size and/or color for each point, so the renderer must
do the extra work of constructing each point individually. In plt.plot, on the other
hand, the points are always essentially clones of each other, so the work of determin‐
ing the appearance of the points is done only once for the entire set of data. For large
datasets, the difference between these two can lead to vastly different performance,
and for this reason, plt.plot should be preferred over plt.scatter for large
datasets.

Visualizing Errors
For any scientific measurement, accurate accounting for errors is nearly as important,
if not more important, than accurate reporting of the number itself. For example,
imagine that I am using some astrophysical observations to estimate the Hubble Con‐
stant, the local measurement of the expansion rate of the universe. I know that the
current literature suggests a value of around 71 (km/s)/Mpc, and I measure a value of
74 (km/s)/Mpc with my method. Are the values consistent? The only correct answer,
given this information, is this: there is no way to know.

Visualizing Errors | 237

Suppose I augment this information with reported uncertainties: the current litera‐
ture suggests a value of around 71 ± 2.5 (km/s)/Mpc, and my method has measured a
value of 74 ± 5 (km/s)/Mpc. Now are the values consistent? That is a question that
can be quantitatively answered.
In visualization of data and results, showing these errors effectively can make a plot
convey much more complete information.

Basic Errorbars
A basic errorbar can be created with a single Matplotlib function call (Figure 4-27):
In[1]: %matplotlib inline
import matplotlib.pyplot as plt
plt.style.use('seaborn-whitegrid')
import numpy as np
In[2]: x = np.linspace(0, 10, 50)
dy = 0.8
y = np.sin(x) + dy * np.random.randn(50)

plt.errorbar(x, y, yerr=dy, fmt='.k');

Figure 4-27. An errorbar example

Here the fmt is a format code controlling the appearance of lines and points, and has
the same syntax as the shorthand used in plt.plot, outlined in “Simple Line Plots”
on page 224 and “Simple Scatter Plots” on page 233.
In addition to these basic options, the errorbar function has many options to fine-
tune the outputs. Using these additional options you can easily customize the aesthet‐
ics of your errorbar plot. I often find it helpful, especially in crowded plots, to make
the errorbars lighter than the points themselves (Figure 4-28):
In[3]: plt.errorbar(x, y, yerr=dy, fmt='o', color='black',
ecolor='lightgray', elinewidth=3, capsize=0);

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Figure 4-28. Customizing errorbars

In addition to these options, you can also specify horizontal errorbars (xerr), one-
sided errorbars, and many other variants. For more information on the options avail‐
able, refer to the docstring of plt.errorbar.

Continuous Errors
In some situations it is desirable to show errorbars on continuous quantities. Though
Matplotlib does not have a built-in convenience routine for this type of application,
it’s relatively easy to combine primitives like plt.plot and plt.fill_between for a
useful result.
Here we’ll perform a simple Gaussian process regression (GPR), using the Scikit-Learn
API (see “Introducing Scikit-Learn” on page 343 for details). This is a method of fit‐
ting a very flexible nonparametric function to data with a continuous measure of the
uncertainty. We won’t delve into the details of Gaussian process regression at this
point, but will focus instead on how you might visualize such a continuous error
measurement:
In[4]: from sklearn.gaussian_process import GaussianProcess

# define the model and draw some data

model = lambda x: x * np.sin(x)
xdata = np.array([1, 3, 5, 6, 8])
ydata = model(xdata)

# Compute the Gaussian process fit

gp = GaussianProcess(corr='cubic', theta0=1e-2, thetaL=1e-4, thetaU=1E-1,
random_start=100)
gp.fit(xdata[:, np.newaxis], ydata)

xfit = np.linspace(0, 10, 1000)

yfit, MSE = gp.predict(xfit[:, np.newaxis], eval_MSE=True)
dyfit = 2 * np.sqrt(MSE) # 2*sigma ~ 95% confidence region

Visualizing Errors | 239

We now have xfit, yfit, and dyfit, which sample the continuous fit to our data. We
could pass these to the plt.errorbar function as above, but we don’t really want to
plot 1,000 points with 1,000 errorbars. Instead, we can use the plt.fill_between
function with a light color to visualize this continuous error (Figure 4-29):
In[5]: # Visualize the result
plt.plot(xdata, ydata, 'or')
plt.plot(xfit, yfit, '-', color='gray')

plt.fill_between(xfit, yfit - dyfit, yfit + dyfit,

color='gray', alpha=0.2)
plt.xlim(0, 10);

Figure 4-29. Representing continuous uncertainty with filled regions

Note what we’ve done here with the fill_between function: we pass an x value, then
the lower y-bound, then the upper y-bound, and the result is that the area between
these regions is filled.
The resulting figure gives a very intuitive view into what the Gaussian process regres‐
sion algorithm is doing: in regions near a measured data point, the model is strongly
constrained and this is reflected in the small model errors. In regions far from a
measured data point, the model is not strongly constrained, and the model errors
increase.
For more information on the options available in plt.fill_between() (and the
closely related plt.fill() function), see the function docstring or the Matplotlib
documentation.
Finally, if this seems a bit too low level for your taste, refer to “Visualization with Sea‐
born” on page 311, where we discuss the Seaborn package, which has a more stream‐
lined API for visualizing this type of continuous errorbar.

240 | Chapter 4: Visualization with Matplotlib