Visualizing Tabular Data
OverviewTeaching: 30 min
Exercises: 20 minQuestions
How can I visualize tabular data in Python?
How can I group several plots together?Objectives
Plot simple graphs from data.
Plot multiple graphs in a single figure.
The mathematician Richard Hamming once said, “The purpose of computing is insight, not numbers,”
and the best way to develop insight is often to visualize data. Visualization deserves an entire
lecture of its own, but we can explore a few features of Python’s
matplotlib library here. While
there is no official plotting library,
matplotlib is the de facto standard. First, we will
pyplot module from
matplotlib and use two of its functions to create and display a
heat map of our data:
If you are continuing in the same notebook from the previous episode, you already have a
datavariable and have imported
numpy. If you are starting a new notebook at this point, you need the following two lines:
import numpy data = numpy.loadtxt(fname='inflammation-01.csv', delimiter=',')
import matplotlib.pyplot image = matplotlib.pyplot.imshow(data) matplotlib.pyplot.show()
Each row in the heat map corresponds to a patient in the clinical trial dataset, and each column corresponds to a day in the dataset. Blue pixels in this heat map represent low values, while yellow pixels represent high values. As we can see, the general number of inflammation flare-ups for the patients rises and falls over a 40-day period.
So far so good as this is in line with our knowledge of the clinical trial and Dr. Maverick’s claims:
- the patients take their medication once their inflammation flare-ups begin
- it takes around 3 weeks for the medication to take effect and begin reducing flare-ups
- and flare-ups appear to drop to zero by the end of the clinical trial.
Now let’s take a look at the average inflammation over time:
ave_inflammation = numpy.mean(data, axis=0) ave_plot = matplotlib.pyplot.plot(ave_inflammation) matplotlib.pyplot.show()
Here, we have put the average inflammation per day across all patients in the variable
ave_inflammation, then asked
matplotlib.pyplot to create and display a line graph of those
values. The result is a reasonably linear rise and fall, in line with Dr. Maverick’s claim that
the medication takes 3 weeks to take effect. But a good data scientist doesn’t just consider the
average of a dataset, so let’s have a look at two other statistics:
max_plot = matplotlib.pyplot.plot(numpy.max(data, axis=0)) matplotlib.pyplot.show()
min_plot = matplotlib.pyplot.plot(numpy.min(data, axis=0)) matplotlib.pyplot.show()
The maximum value rises and falls linearly, while the minimum seems to be a step function. Neither trend seems particularly likely, so either there’s a mistake in our calculations or something is wrong with our data. This insight would have been difficult to reach by examining the numbers themselves without visualization tools.
You can group similar plots in a single figure using subplots.
This script below uses a number of new commands. The function
creates a space into which we will place all of our plots. The parameter
tells Python how big to make this space. Each subplot is placed into the figure using
add_subplot method. The
add_subplot method takes
3 parameters. The first denotes how many total rows of subplots there are, the second parameter
refers to the total number of subplot columns, and the final parameter denotes which subplot
your variable is referencing (left-to-right, top-to-bottom). Each subplot is stored in a
different variable (
axes3). Once a subplot is created, the axes can
be titled using the
set_xlabel() command (or
Here are our three plots side by side:
import numpy import matplotlib.pyplot data = numpy.loadtxt(fname='inflammation-01.csv', delimiter=',') fig = matplotlib.pyplot.figure(figsize=(10.0, 3.0)) axes1 = fig.add_subplot(1, 3, 1) axes2 = fig.add_subplot(1, 3, 2) axes3 = fig.add_subplot(1, 3, 3) axes1.set_ylabel('average') axes1.plot(numpy.mean(data, axis=0)) axes2.set_ylabel('max') axes2.plot(numpy.max(data, axis=0)) axes3.set_ylabel('min') axes3.plot(numpy.min(data, axis=0)) fig.tight_layout() matplotlib.pyplot.savefig('inflammation.png') matplotlib.pyplot.show()
The call to
loadtxt reads our data,
and the rest of the program tells the plotting library
how large we want the figure to be,
that we’re creating three subplots,
what to draw for each one,
and that we want a tight layout.
(If we leave out that call to
the graphs will actually be squeezed together more closely.)
The call to
savefig stores the plot as a graphics file. This can be
a convenient way to store your plots for use in other documents, web
pages etc. The graphics format is automatically determined by
Matplotlib from the file name ending we specify; here PNG from
‘inflammation.png’. Matplotlib supports many different graphics
formats, including SVG, PDF, and JPEG.
Importing libraries with shortcuts
In this lesson we use the
import matplotlib.pyplotsyntax to import the
matplotlib. However, shortcuts such as
import matplotlib.pyplot as pltare frequently used. Importing
pyplotthis way means that after the initial import, rather than writing
matplotlib.pyplot.plot(...), you can now write
plt.plot(...). Another common convention is to use the shortcut
import numpy as npwhen importing the NumPy library. We then can write
numpy.loadtxt(...), for example.
Some people prefer these shortcuts as it is quicker to type and results in shorter lines of code - especially for libraries with long names! You will frequently see Python code online using a
plt, or a NumPy function with
np, and it’s because they’ve used this shortcut. It makes no difference which approach you choose to take, but you must be consistent as if you use
import matplotlib.pyplot as pltthen
matplotlib.pyplot.plot(...)will not work, and you must use
plt.plot(...)instead. Because of this, when working with other people it is important you agree on how libraries are imported.
Why do all of our plots stop just short of the upper end of our graph?
Because matplotlib normally sets x and y axes limits to the min and max of our data (depending on data range)
If we want to change this, we can use the
set_ylim(min, max)method of each ‘axes’, for example:
Update your plotting code to automatically set a more appropriate scale. (Hint: you can make use of the
minmethods to help.)
# One method axes3.set_ylabel('min') axes3.plot(numpy.min(data, axis=0)) axes3.set_ylim(0,6)
# A more automated approach min_data = numpy.min(data, axis=0) axes3.set_ylabel('min') axes3.plot(min_data) axes3.set_ylim(numpy.min(min_data), numpy.max(min_data) * 1.1)
Drawing Straight Lines
In the center and right subplots above, we expect all lines to look like step functions because non-integer value are not realistic for the minimum and maximum values. However, you can see that the lines are not always vertical or horizontal, and in particular the step function in the subplot on the right looks slanted. Why is this?
Because matplotlib interpolates (draws a straight line) between the points. One way to do avoid this is to use the Matplotlib
import numpy import matplotlib.pyplot data = numpy.loadtxt(fname='inflammation-01.csv', delimiter=',') fig = matplotlib.pyplot.figure(figsize=(10.0, 3.0)) axes1 = fig.add_subplot(1, 3, 1) axes2 = fig.add_subplot(1, 3, 2) axes3 = fig.add_subplot(1, 3, 3) axes1.set_ylabel('average') axes1.plot(numpy.mean(data, axis=0), drawstyle='steps-mid') axes2.set_ylabel('max') axes2.plot(numpy.max(data, axis=0), drawstyle='steps-mid') axes3.set_ylabel('min') axes3.plot(numpy.min(data, axis=0), drawstyle='steps-mid') fig.tight_layout() matplotlib.pyplot.show()
Make Your Own Plot
Create a plot showing the standard deviation (
numpy.std) of the inflammation data for each day across all patients.
std_plot = matplotlib.pyplot.plot(numpy.std(data, axis=0)) matplotlib.pyplot.show()
Moving Plots Around
Modify the program to display the three plots on top of one another instead of side by side.
import numpy import matplotlib.pyplot data = numpy.loadtxt(fname='inflammation-01.csv', delimiter=',') # change figsize (swap width and height) fig = matplotlib.pyplot.figure(figsize=(3.0, 10.0)) # change add_subplot (swap first two parameters) axes1 = fig.add_subplot(3, 1, 1) axes2 = fig.add_subplot(3, 1, 2) axes3 = fig.add_subplot(3, 1, 3) axes1.set_ylabel('average') axes1.plot(numpy.mean(data, axis=0)) axes2.set_ylabel('max') axes2.plot(numpy.max(data, axis=0)) axes3.set_ylabel('min') axes3.plot(numpy.min(data, axis=0)) fig.tight_layout() matplotlib.pyplot.show()
pyplotmodule from the
matplotliblibrary for creating simple visualizations.