Resources for teaching & learning practical data visualization with python.

Last update: Sep 24, 2022

Overview

Practical Data Visualization with Python

Overview

All views expressed on this site are my own and do not represent the opinions of any entity with which I have been, am now, or will be affiliated.

This repository contains all materials related to a lecture / seminar I teach on practical data visualization with python. What I mean by "practical" is that the materials herein do not focus on one particular library or data visualization method; rather, my goal is to empower the consumer of this content with the tools, heuristics, and methods needed to handle a wide variety of data visualization problems.

If you have questions, comments, or suggested alterations to these materials, please open an issue here on GitHub. Also, don't hesitate to reach out via LinkedIn.

Outline of Materials

Below you'll find a brief outline of the content contained in the four sections of this seminar, along with notebook links, and an example visualization from each section. For each section there is a separate notebook of python code containing all the materials for that section. Each notebook will start with a few setup steps--package imports and data prep mostly--that are almost identical between the notebooks, directly after which comes the content for each section. For information about the data used in these materials, check out the data_prep_nb.ipynb notebook, the easy-to-view version of which is hosted here.

Section 1: Why We Visualize

Here is the link to the easy-to-view notebook for this section of material.
Here is the link to the GitHub-hosted notebook for this section of the material.

The power of visual data representation and storytelling.
A few principles and heuristics of visualization.
The building blocks of visualization explored.

Example Visualization from this Section:

Section 2: Overview of Python Visualization Landscape

Here is the link to the easy-to-view notebook for this section of material.
Here is the link to the GitHub-hosted notebook for this section of the material.

Intro to the visualization ecosystem: python's Tower of Babel.
Smorgasbord of packages explored through a single example viz.
Quick & dirty (and subjective) heuristics for picking a visualization package.

Example Visualization from this Section:

Section 3: Statistical Visualization in the Wild

Here is the link to the easy-to-view notebook for this section of material.
Here is the link to the GitHub-hosted notebook for this section of the material.

Example business use case of data visualization:
1. Observational:
  - mean, median, and variance
  - distributions
2. Inferential:
  - parametric tests
  - non-parametric tests

Example Visualization from this Section:

Section 4: Library Deep-Dive (Plotly)

Here is the link to the easy-to-view notebook for this section of material.
Here is the link to the GitHub-hosted notebook for this section of the material.

Quick and simple data visualizations with Plotly Express.
Additional control and complexity with base Plotly.

Example Visualization from this Section:

Homework Exercises

There is a homework associated with these materials, for those interested. Given the open-ended nature of the homework, there is no answer key. That said, if you're working through it and would like some feedback, feel free to reach out to me via LinkedIn.

Here is the link to the easy-to-view homework notebook.
Here is the link to the GitHub-hosted version of the homework notebook.

Setup Instructions

clone this repository
create a virtual environment using python3 -m venv env
- additional information about this can be found here
activate that virtual environment using source env/bin/activate
install needed packages using pip install -r requirements.txt
- additional information about this can be found here
run an instance of jupyter lab out of your virutal env using env/bin/jupyter-lab
open and run the four main files of content for this course--one for each section:
- part_1_main_nb.ipynb
- part_2_main_nb.ipynb
- part_3_main_nb.ipynb
- part_4_main_nb.ipynb

Comments

Main 4 Sections of Content

Note to self as validation:

For section 3 -- Statistical Visualization in the Wild -- I plan on telling a story surrounding the DTI distributional shift from beginning to end of 2017. This distributional shift can be seen in the QnD image below I build as validation of my hunch when pulling the data. The orange is the late 2017 DTI distro and the blue is the early 2017 DTI distro.
documentation

opened by pmaji 4
Bump nbconvert from 5.5.0 to 6.3.0
Bumps nbconvert from 5.5.0 to 6.3.0.

Commits

cefe0bf Release 6.3.0

a534fb9 Release 6.3.0b0

87920c5 Add changelog for 6.3.0 (#1669)

dd6d9c7 add slide numbering (#1654)

5d2c5e2 Update state filter (#1664)

11ea593 fix: avoid closing the script tag early by escaping a forward slash (#1665)

968c5fb Fix HTML templates mentioned in help docs (#1653)

35c4d07 Add a new output filter that excludes widgets if there is no state (#1643)

c663c75 6.2.0

fd1dd15 6.2.0rc2

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dependencies
opened by dependabot[bot] 1
Bump notebook from 6.1.5 to 6.4.10
Bumps notebook from 6.1.5 to 6.4.10.

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dependencies
opened by dependabot[bot] 1
Bump notebook from 6.1.5 to 6.4.1
Bumps notebook from 6.1.5 to 6.4.1.

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dependencies
opened by dependabot[bot] 1
Bump urllib3 from 1.25.3 to 1.25.8
Bumps urllib3 from 1.25.3 to 1.25.8.

Release notes

Sourced from urllib3's releases.

1.25.8

Release: 1.25.8

1.25.7

No release notes provided.

1.25.6

Release: 1.25.6

1.25.5

Release: 1.25.5

1.25.4

Release: 1.25.4

Changelog

Sourced from urllib3's changelog.

1.25.8 (2020-01-20)

Drop support for EOL Python 3.4 (Pull #1774)

Optimize _encode_invalid_chars (Pull #1787)

1.25.7 (2019-11-11)

Preserve chunked parameter on retries (Pull #1715, Pull #1734)

Allow unset SERVER_SOFTWARE in App Engine (Pull #1704, Issue #1470)

Fix issue where URL fragment was sent within the request target. (Pull #1732)

Fix issue where an empty query section in a URL would fail to parse. (Pull #1732)

Remove TLS 1.3 support in SecureTransport due to Apple removing support (Pull #1703)

1.25.6 (2019-09-24)

Fix issue where tilde (~) characters were incorrectly percent-encoded in the path. (Pull #1692)

1.25.5 (2019-09-19)

Add mitigation for BPO-37428 affecting Python <3.7.4 and OpenSSL 1.1.1+ which caused certificate verification to be enabled when using cert_reqs=CERT_NONE. (Issue #1682)

1.25.4 (2019-09-19)

Propagate Retry-After header settings to subsequent retries. (Pull #1607)

Fix edge case where Retry-After header was still respected even when explicitly opted out of. (Pull #1607)

Remove dependency on rfc3986 for URL parsing.

Fix issue where URLs containing invalid characters within Url.auth would raise an exception instead of percent-encoding those characters.

... (truncated)

Commits

2a57bc5 Release 1.25.8 (#1788)

a2697e7 Optimize _encode_invalid_chars (#1787)

d2a5a59 Move IPv6 test skips in server fixtures

d44f0e5 Factorize test certificates serialization

84abc7f Generate IPV6 certificates using trustme

6a15b18 Run IPv6 Tornado server from fixture

4903840 Use trustme to generate IP_SAN cert

9971e27 Empty responses should have no lines.

62ef68e Use trustme to generate NO_SAN certs

fd2666e Use fixture to configure NO_SAN test certs

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dependencies
opened by dependabot[bot] 1
Bump jupyter-core from 4.5.0 to 4.11.2
Bumps jupyter-core from 4.5.0 to 4.11.2.

Release notes

Sourced from jupyter-core's releases.

4.11.1

What's Changed

Fix inclusion of jupyter file and check in CI by @blink1073 in jupyter/jupyter_core#276

Full Changelog: https://github.com/jupyter/jupyter_core/compare/4.11.0...4.11.1

4.11.0

What's Changed

Use hatch backend by @blink1073 in jupyter/jupyter_core#265

is_hidden: Use normalized paths by @martinRenou in jupyter/jupyter_core#271

New Contributors

@martinRenou made their first contribution in jupyter/jupyter_core#271

Full Changelog: https://github.com/jupyter/jupyter_core/compare/4.10.0...4.11.0

4.10.0

What's Changed

Update changelog for 4.9.2 by @blink1073 in jupyter/jupyter_core#252

Include all files from jupyter_core by @jonringer in jupyter/jupyter_core#253

Add project URLs to setup.cfg by @tlinhart in jupyter/jupyter_core#254

Set up pre-commit by @blink1073 in jupyter/jupyter_core#255

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in jupyter/jupyter_core#257

Add flake8 and mypy settings by @blink1073 in jupyter/jupyter_core#256

Clean up CI by @blink1073 in jupyter/jupyter_core#258

Update changelog for 4.10 Release by @blink1073 in jupyter/jupyter_core#259

New Contributors

@jonringer made their first contribution in jupyter/jupyter_core#253

@tlinhart made their first contribution in jupyter/jupyter_core#254

@pre-commit-ci made their first contribution in jupyter/jupyter_core#257

Full Changelog: https://github.com/jupyter/jupyter_core/compare/4.9.2...4.10.0

4.9.2

What's Changed

set proper sys.argv[0] for subcommand by @bnavigator in jupyter/jupyter_core#248

Add explicit encoding in open calls by @dlukes in jupyter/jupyter_core#249

jupyter_config_dir - reorder home_dir initialization by @dharmaquark in jupyter/jupyter_core#251

New Contributors

@bnavigator made their first contribution in jupyter/jupyter_core#248

@dlukes made their first contribution in jupyter/jupyter_core#249

@dharmaquark made their first contribution in jupyter/jupyter_core#251

Full Changelog: https://github.com/jupyter/jupyter_core/compare/4.9.1...4.9.2

Changelog

Sourced from jupyter-core's changelog.

Changes in jupyter-core

5.0.0

(Full Changelog)

Major Changes

Prefer Environment Level Configuration

We now make the assumption that if we are running in a virtual environment, we should prioritize the environment-level sys.prefix over the user-level paths. Users can opt out of this behavior by setting JUPYTER_PREFER_ENV_PATH, which takes precedence over our autodetection.

Migrate to Standard Platform Directories

In version 5, we introduce a JUPYTER_PLATFORM_DIRS environment variable to opt in to using more appropriate platform-specific directories. We raise a deprecation warning if the variable is not set. In version 6, JUPYTER_PLATFORM_DIRS will be opt-out. In version 7, we will remove the environment variable checks and old directory logic.

Drop Support for Python 3.7

We are dropping support for Python 3.7 ahead of its official end of life, to reduce maintenance burden as we add support for Python 3.11.

Enhancements made

Use platformdirs for path locations #292 (@blink1073)

Try to detect if we are in a virtual environment and change path precedence accordingly #286 (@jasongrout)

Bugs fixed

Add current working directory as first config path #291 (@blink1073)

Fix inclusion of jupyter file and check in CI #276 (@blink1073)

Maintenance and upkeep improvements

Bump github/codeql-action from 1 to 2 #308 (@dependabot)

Bump actions/checkout from 2 to 3 #307 (@dependabot)

Add dependabot #306 (@blink1073)

Adopt jupyter releaser #305 (@blink1073)

Add more typing #304 (@blink1073)

Require Python 3.8+ #302 (@blink1073)

Use hatch backend #265 (@blink1073)

Switch to flit build backend #262 (@blink1073)

is_hidden: Use normalized paths #271 (@martinRenou)

Documentation

Update broken link to Contributing guide #289 (@jamesr66a)

Contributors to this release

... (truncated)

Commits

a8eac8c Release 4.11.2

1118c8c Merge pull request from GHSA-m678-f26j-3hrp

d3f61f3 Release 4.11.1

e7eeb9e Fix inclusion of jupyter file and check in CI (#276)

035bf11 Release 4.11.0

45aa28b [pre-commit.ci] pre-commit autoupdate (#273)

73401cc [pre-commit.ci] pre-commit autoupdate (#272)

bc6b771 is_hidden: Use normalized paths (#271)

be38e52 [pre-commit.ci] pre-commit autoupdate (#270)

7b790d8 [pre-commit.ci] pre-commit autoupdate (#269)

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dependencies
opened by dependabot[bot] 0
Bump joblib from 0.13.2 to 1.2.0
Bumps joblib from 0.13.2 to 1.2.0.

Changelog

Sourced from joblib's changelog.

Release 1.2.0

Fix a security issue where eval(pre_dispatch) could potentially run arbitrary code. Now only basic numerics are supported. joblib/joblib#1327

Make sure that joblib works even when multiprocessing is not available, for instance with Pyodide joblib/joblib#1256

Avoid unnecessary warnings when workers and main process delete the temporary memmap folder contents concurrently. joblib/joblib#1263

Fix memory alignment bug for pickles containing numpy arrays. This is especially important when loading the pickle with mmap_mode != None as the resulting numpy.memmap object would not be able to correct the misalignment without performing a memory copy. This bug would cause invalid computation and segmentation faults with native code that would directly access the underlying data buffer of a numpy array, for instance C/C++/Cython code compiled with older GCC versions or some old OpenBLAS written in platform specific assembly. joblib/joblib#1254

Vendor cloudpickle 2.2.0 which adds support for PyPy 3.8+.

Vendor loky 3.3.0 which fixes several bugs including:

robustly forcibly terminating worker processes in case of a crash (joblib/joblib#1269);

avoiding leaking worker processes in case of nested loky parallel calls;

reliability spawn the correct number of reusable workers.

Release 1.1.0

Fix byte order inconsistency issue during deserialization using joblib.load in cross-endian environment: the numpy arrays are now always loaded to use the system byte order, independently of the byte order of the system that serialized the pickle. joblib/joblib#1181

Fix joblib.Memory bug with the ignore parameter when the cached function is a decorated function.

... (truncated)

Commits

5991350 Release 1.2.0

3fa2188 MAINT cleanup numpy warnings related to np.matrix in tests (#1340)

cea26ff CI test the future loky-3.3.0 branch (#1338)

8aca6f4 MAINT: remove pytest.warns(None) warnings in pytest 7 (#1264)

067ed4f XFAIL test_child_raises_parent_exits_cleanly with multiprocessing (#1339)

ac4ebd5 MAINT add back pytest warnings plugin (#1337)

a23427d Test child raises parent exits cleanly more reliable on macos (#1335)

ac09691 [MAINT] various test updates (#1334)

4a314b1 Vendor loky 3.2.0 (#1333)

bdf47e9 Make test_parallel_with_interactively_defined_functions_default_backend timeo...

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dependencies
opened by dependabot[bot] 0
Bump nbconvert from 5.5.0 to 6.5.1
Bumps nbconvert from 5.5.0 to 6.5.1.

Release notes

Sourced from nbconvert's releases.

Release 6.5.1

No release notes provided.

6.5.0

What's Changed

Drop dependency on testpath. by @anntzer in jupyter/nbconvert#1723

Adopt pre-commit by @blink1073 in jupyter/nbconvert#1744

Add pytest settings and handle warnings by @blink1073 in jupyter/nbconvert#1745

Apply Autoformatters by @blink1073 in jupyter/nbconvert#1746

Add git-blame-ignore-revs by @blink1073 in jupyter/nbconvert#1748

Update flake8 config by @blink1073 in jupyter/nbconvert#1749

support bleach 5, add packaging and tinycss2 dependencies by @bollwyvl in jupyter/nbconvert#1755

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in jupyter/nbconvert#1752

update cli example by @leahecole in jupyter/nbconvert#1753

Clean up pre-commit by @blink1073 in jupyter/nbconvert#1757

Clean up workflows by @blink1073 in jupyter/nbconvert#1750

New Contributors

@pre-commit-ci made their first contribution in jupyter/nbconvert#1752

Full Changelog: https://github.com/jupyter/nbconvert/compare/6.4.5...6.5

6.4.3

What's Changed

Add section to customizing showing how to use template inheritance by @stefanv in jupyter/nbconvert#1719

Remove ipython genutils by @rgs258 in jupyter/nbconvert#1727

Update changelog for 6.4.3 by @blink1073 in jupyter/nbconvert#1728

New Contributors

@stefanv made their first contribution in jupyter/nbconvert#1719

@rgs258 made their first contribution in jupyter/nbconvert#1727

Full Changelog: https://github.com/jupyter/nbconvert/compare/6.4.2...6.4.3

6.4.0

What's Changed

Optionally speed up validation by @gwincr11 in jupyter/nbconvert#1672

Adding missing div compared to JupyterLab DOM structure by @SylvainCorlay in jupyter/nbconvert#1678

Allow passing extra args to code highlighter by @yuvipanda in jupyter/nbconvert#1683

Prevent page breaks in outputs when printing by @SylvainCorlay in jupyter/nbconvert#1679

Add collapsers to template by @SylvainCorlay in jupyter/nbconvert#1689

Fix recent pandoc latex tables by adding calc and array (#1536, #1566) by @cgevans in jupyter/nbconvert#1686

Add an invalid notebook error by @gwincr11 in jupyter/nbconvert#1675

Fix typos in execute.py by @TylerAnderson22 in jupyter/nbconvert#1692

Modernize latex greek math handling (partially fixes #1673) by @cgevans in jupyter/nbconvert#1687

Fix use of deprecated API and update test matrix by @blink1073 in jupyter/nbconvert#1696

Update nbconvert_library.ipynb by @letterphile in jupyter/nbconvert#1695

Changelog for 6.4 by @blink1073 in jupyter/nbconvert#1697

New Contributors

... (truncated)

Commits

7471b75 Release 6.5.1

c1943e0 Fix pre-commit

8685e93 Fix tests

0abf290 Run black and prettier

418d545 Run test on 6.x branch

bef65d7 Convert input to string prior to escape HTML

0818628 Check input type before escaping

b206470 GHSL-2021-1017, GHSL-2021-1020, GHSL-2021-1021

a03cbb8 GHSL-2021-1026, GHSL-2021-1025

48fe71e GHSL-2021-1024

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dependencies
opened by dependabot[bot] 0
Bump mistune from 0.8.4 to 2.0.3
Bumps mistune from 0.8.4 to 2.0.3.

Release notes

Sourced from mistune's releases.

Version 2.0.2

Fix escape_url via lepture/mistune#295

Version 2.0.1

Fix XSS for image link syntax.

Version 2.0.0

First release of Mistune v2.

Version 2.0.0 RC1

In this release, we have a Security Fix for harmful links.

Version 2.0.0 Alpha 1

This is the first release of v2. An alpha version for users to have a preview of the new mistune.

Changelog

Sourced from mistune's changelog.

Changelog

Here is the full history of mistune v2.

Version 2.0.4

Released on Jul 15, 2022 Fix url plugin in <a> tag Fix * formatting
Version 2.0.3

Released on Jun 27, 2022

Fix table plugin

Security fix for CVE-2022-34749

Version 2.0.2

Released on Jan 14, 2022 Fix escape_url
Version 2.0.1

Released on Dec 30, 2021

XSS fix for image link syntax.

Version 2.0.0

Released on Dec 5, 2021 This is the first non-alpha release of mistune v2.
Version 2.0.0rc1

Released on Feb 16, 2021

Version 2.0.0a6

</tr></table>

... (truncated)

Commits

3f422f1 Version bump 2.0.3

a6d4321 Fix asteris emphasis regex CVE-2022-34749

5638e46 Merge pull request #307 from jieter/patch-1

0eba471 Fix typo in guide.rst

61e9337 Fix table plugin

76dec68 Add documentation for renderer heading when TOC enabled

799cd11 Version bump 2.0.2

babb0cf Merge pull request #295 from dairiki/bug.escape_url

fc2cd53 Make mistune.util.escape_url less aggressive

3e8d352 Version bump 2.0.1

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dependencies
opened by dependabot[bot] 0
Bump numpy from 1.16.4 to 1.22.0
Bumps numpy from 1.16.4 to 1.22.0.

Release notes

Sourced from numpy's releases.

v1.22.0

NumPy 1.22.0 Release Notes

NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.

A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.

NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.

New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.

A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

Expired deprecations

Deprecated numeric style dtype strings have been removed

Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

(gh-19539)

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

(gh-19615)

... (truncated)

Commits

4adc87d Merge pull request #20685 from charris/prepare-for-1.22.0-release

fd66547 REL: Prepare for the NumPy 1.22.0 release.

125304b wip

c283859 Merge pull request #20682 from charris/backport-20416

5399c03 Merge pull request #20681 from charris/backport-20954

f9c45f8 Merge pull request #20680 from charris/backport-20663

794b36f Update armccompiler.py

d93b14e Update test_public_api.py

7662c07 Update init.py

311ab52 Update armccompiler.py

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dependencies
opened by dependabot[bot] 0
Bump notebook from 6.1.5 to 6.4.12
⚠️ Dependabot is rebasing this PR ⚠️

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Bumps notebook from 6.1.5 to 6.4.12.

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dependencies
opened by dependabot[bot] 0
Bump certifi from 2019.6.16 to 2022.12.7
Bumps certifi from 2019.6.16 to 2022.12.7.

Commits

9e9e840 2022.12.07

b81bdb2 2022.09.24

939a28f 2022.09.14

aca828a 2022.06.15.2

de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ...

b8eb5e9 2022.06.15.1

47fb7ab Fix deprecation warning on Python 3.11 (#199)

b0b48e0 fixes #198 -- update link in license

9d514b4 2022.06.15

4151e88 Add py.typed to MANIFEST.in to package in sdist (#196)

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dependencies
opened by dependabot[bot] 0