Published

January 18, 2025

Modified

November 22, 2024

Note

Figures don’t seem to be cross-referencing across documents. Let’s see if they work within documents.

Does the link to Figure 1 work?

How about Figure 2?

Apparently so.

Okay, so do the ggplot2 figures work in this document? Specifically, does the reference to ?@fig-dual-boxplots-diff-ggplot2 work?

No. So, the issue is cross-document figure references.

About

This page provides a very basic introduction to Python and the matplotlib plotting library.

Why Python?

Python is an awesome language for data science and data visualization. It is more popular than R, and it is widely used in scientific research and in industry.

I find that it has a very readable syntax, meaning that it’s relatively easy to see what well-written Python code is doing.

Setup

We start by importing the numpy and pyplot libraries and giving them convenient short names for future reference.

Code 
import numpy as np
import matplotlib.pyplot as plt

Plotting one variable

Continuous

Histograms

From https://matplotlib.org/stable/gallery/statistics/hist.html#sphx-glr-gallery-statistics-hist-py

Load components from matplotlib.

Code 
from matplotlib import colors
from matplotlib.ticker import PercentFormatter

# Create a random number generator with a fixed seed for reproducibility
rng = np.random.default_rng(19680801)

Generate data and render it.

Code 
N_points = 100000
n_bins = 20

# Generate two normal distributions
dist1 = rng.standard_normal(N_points)
dist2 = 0.4 * rng.standard_normal(N_points) + 5

fig, axs = plt.subplots(1, 2, sharey=True, tight_layout=True)

# We can set the number of bins with the *bins* keyword argument.
axs[0].hist(dist1, bins=n_bins)
axs[1].hist(dist2, bins=n_bins)

plt.show()
Figure 1: Two histograms with 100K points each.

Violin

Violin plots are another way to depict the distribution of a single continuous variable.

The following code is copied verbatim from the following site:

https://matplotlib.org/stable/gallery/statistics/violinplot.html

Code 
# fake data
fs = 10  # fontsize
pos = [1, 2, 4, 5, 7, 8]
data = [np.random.normal(0, std, size=100) for std in pos]

# Create a plot with 2 rows and 6 columns
fig, axs = plt.subplots(nrows=2, ncols=6, figsize=(10, 4))

axs[0, 0].violinplot(data, pos, points=20, widths=0.3,
                     showmeans=True, showextrema=True, showmedians=True)
axs[0, 0].set_title('Custom violin 1', fontsize=fs)

axs[0, 1].violinplot(data, pos, points=40, widths=0.5,
                     showmeans=True, showextrema=True, showmedians=True,
                     bw_method='silverman')
axs[0, 1].set_title('Custom violin 2', fontsize=fs)

axs[0, 2].violinplot(data, pos, points=60, widths=0.7, showmeans=True,
                     showextrema=True, showmedians=True, bw_method=0.5)
axs[0, 2].set_title('Custom violin 3', fontsize=fs)

axs[0, 3].violinplot(data, pos, points=60, widths=0.7, showmeans=True,
                     showextrema=True, showmedians=True, bw_method=0.5,
                     quantiles=[[0.1], [], [], [0.175, 0.954], [0.75], [0.25]])
axs[0, 3].set_title('Custom violin 4', fontsize=fs)

axs[0, 4].violinplot(data[-1:], pos[-1:], points=60, widths=0.7,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[0.05, 0.1, 0.8, 0.9], bw_method=0.5)
axs[0, 4].set_title('Custom violin 5', fontsize=fs)

axs[0, 5].violinplot(data[-1:], pos[-1:], points=60, widths=0.7,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[0.05, 0.1, 0.8, 0.9], bw_method=0.5, side='low')

axs[0, 5].violinplot(data[-1:], pos[-1:], points=60, widths=0.7,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[0.05, 0.1, 0.8, 0.9], bw_method=0.5, side='high')
axs[0, 5].set_title('Custom violin 6', fontsize=fs)

axs[1, 0].violinplot(data, pos, points=80, vert=False, widths=0.7,
                     showmeans=True, showextrema=True, showmedians=True)
axs[1, 0].set_title('Custom violin 7', fontsize=fs)

axs[1, 1].violinplot(data, pos, points=100, vert=False, widths=0.9,
                     showmeans=True, showextrema=True, showmedians=True,
                     bw_method='silverman')
axs[1, 1].set_title('Custom violin 8', fontsize=fs)

axs[1, 2].violinplot(data, pos, points=200, vert=False, widths=1.1,
                     showmeans=True, showextrema=True, showmedians=True,
                     bw_method=0.5)
axs[1, 2].set_title('Custom violin 9', fontsize=fs)

axs[1, 3].violinplot(data, pos, points=200, vert=False, widths=1.1,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[[0.1], [], [], [0.175, 0.954], [0.75], [0.25]],
                     bw_method=0.5)
axs[1, 3].set_title('Custom violin 10', fontsize=fs)

axs[1, 4].violinplot(data[-1:], pos[-1:], points=200, vert=False, widths=1.1,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[0.05, 0.1, 0.8, 0.9], bw_method=0.5)
axs[1, 4].set_title('Custom violin 11', fontsize=fs)

axs[1, 5].violinplot(data[-1:], pos[-1:], points=200, vert=False, widths=1.1,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[0.05, 0.1, 0.8, 0.9], bw_method=0.5, side='low')

axs[1, 5].violinplot(data[-1:], pos[-1:], points=200, vert=False, widths=1.1,
                     showmeans=True, showextrema=True, showmedians=True,
                     quantiles=[0.05, 0.1, 0.8, 0.9], bw_method=0.5, side='high')
axs[1, 5].set_title('Custom violin 12', fontsize=fs)


for ax in axs.flat:
    ax.set_yticklabels([])

fig.suptitle("Violin Plotting Examples")
fig.subplots_adjust(hspace=0.4)
plt.show()
Figure 2: Multiple violin plots with different parameters.

Boxplot

From https://matplotlib.org/stable/plot_types/stats/boxplot_plot.html#sphx-glr-plot-types-stats-boxplot-plot-py.

Code 
plt.style.use('_mpl-gallery')

# make data:
np.random.seed(10)
D = np.random.normal((3, 5, 4), (1.25, 1.00, 1.25), (100, 3))

# plot
fig, ax = plt.subplots()
VP = ax.boxplot(D, positions=[2, 4, 6], widths=1.5, patch_artist=True,
                showmeans=False, showfliers=False,
                medianprops={"color": "white", "linewidth": 0.5},
                boxprops={"facecolor": "C0", "edgecolor": "white",
                          "linewidth": 0.5},
                whiskerprops={"color": "C0", "linewidth": 1.5},
                capprops={"color": "C0", "linewidth": 1.5})

ax.set(xlim=(0, 8), xticks=np.arange(1, 8),
       ylim=(0, 8), yticks=np.arange(1, 8))

plt.show()
Figure 3: Example of several boxplots with whiskers.

Discrete/nominal

Bar chart

Source: https://matplotlib.org/stable/plot_types/basic/bar.html#sphx-glr-plot-types-basic-bar-py

Code 
plt.style.use('_mpl-gallery')

# make data:
x = 0.5 + np.arange(8)
y = [4.8, 5.5, 3.5, 4.6, 6.5, 6.6, 2.6, 3.0]

# plot
fig, ax = plt.subplots()

ax.bar(x, y, width=1, edgecolor="white", linewidth=0.7)

ax.set(xlim=(0, 8), xticks=np.arange(1, 8),
       ylim=(0, 8), yticks=np.arange(1, 8))

plt.show()
Figure 4: Example of a bar plot.

Plotting two variables

Scatter plots

Other kinds of plots

The following is copied verbatim from the Quarto website:

https://quarto.org/docs/get-started/hello/vscode.html

For a demonstration of a line plot on a polar axis, see Figure 5.

Code 
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
Figure 5: A line plot on a polar axis