# Introduction to Python

URL to this page: https://hackmd.io/@k8hertweck/introPython

**Sign in to each class meeting** [here](https://goo.gl/forms/j4MbWJuPoIYeJET12)

Have you installed Anaconda and run the conda script to add plotnine? Instructions [here](https://github.com/fredhutchio/fredhutch.io/blob/gh-pages/software.md#python), command to install plotnine:`conda install -c conda-forge plotnine`

This page is for easy access to links we'll use during class. You don't need to do anything with this information until directed by your instructor. Links to the instructor's script will be added as the course progresses.

If you have feedback about this course, please [comment here](https://goo.gl/forms/Bw8dTV0Wghq2iG5i2)

Complete class notes [here](https://github.com/fredhutchio/python_intro)

Instructors:

## Class 1: Intro to Python and Jupyter Notebooks

* [Instructor's notebook from class 1](https://nbviewer.jupyter.org/github/fredhutchio/python_intro/blob/master/class1.ipynb)
* [example notebook](https://github.com/rasilab/machkovech_2018/blob/master/scripts/NA43_competition.ipynb)
* [python style guide](https://www.python.org/dev/peps/pep-0008/)
* [glossary of Python terms](https://www.codecademy.com/articles/glossary-python)
* [guide to Markdown syntax](https://www.markdownguide.org/basic-syntax/)

## Class 2: Working with data

* [Instructor's notebook from class 2](https://nbviewer.jupyter.org/github/fredhutchio/python_intro/blob/master/class2.ipynb)
* URL for direct download into Python from GitHub: https://raw.githubusercontent.com/fredhutchio/R_intro/master/extra/clinical.csv
* Other example data files:
example1: https://raw.githubusercontent.com/fredhutchio/R_intro/master/extra/clinical.tsv
example2: https://raw.githubusercontent.com/fredhutchio/R_intro/master/extra/clinical.txt
* If you have trouble downloading the data from the links above using code, please download the [zipped data file](https://www.dropbox.com/s/k639bkse64r0bfz/data.zip): download, unzip, add three files to data/ in project directory
* [Pandas cheatsheet](https://github.com/pandas-dev/pandas/raw/master/doc/cheatsheet/Pandas_Cheat_Sheet.pdf)

## Class 3: Extracting data from data frames

* [Instructor's notebook from class 3](https://nbviewer.jupyter.org/github/fredhutchio/python_intro/blob/master/class3.ipynb)
* more information on [plotting with pandas](https://towardsdatascience.com/5-minute-guide-to-plotting-with-pandas-e8c0f40a1df4)
* [matplotlib documentation](https://matplotlib.org) (an additional option for plotting)

## Class 4: Data visualization

* [Instructor's notebook](https://nbviewer.jupyter.org/github/fredhutchio/python_intro/blob/master/class4.ipynb)
* [plotnine documentation](https://plotnine.readthedocs.io/en/stable/index.html)
* [ggplot2 documentation](https://ggplot2.tidyverse.org/reference/index.html) - for R users
* [TCGA study abbreviations](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations)

### Other visualization tools for Python

* [matplotlib](https://matplotlib.org/) - the standard Python library for producing high-quality figures with a more imperative approach
* [Altair](https://altair-viz.github.io/) - a declarative visualization toolkit with a similar approach to figure construction as ggplot

## Resources for continued learning

* Learn about other courses through fredhutch.io [here](http://www.fredhutch.io/resources/). Intermediate Python: Programming includes more content on programming structures like loops and functions
* The Fred Hutch Bioinformatics and Data Science Cooperative, or Coop, hosts many community meetings and office hours about data science. Learn more information about these groups [here](https://sciwiki.fredhutch.org/scicomputing/reference_training/#community-groups)
* Join the [Coop Community Slack](https://join.slack.com/t/fhbig/shared_invite/enQtMzUyMDIxNzk3MDU3LWE5NGUyMTY1NGU0N2VmMmEyNTM5YzM1MmNlMTk2YmM1OWNkMmJiNTQxMTQ4OTNkMTFjMjk3M2Q0MzkwYzQ3NDA) to talk about data science with other Hutch researchers. There is a channel specific to discussion about Python!
* The [Fred Hutch Biomedical Data Science Wiki](https://sciwiki.fredhutch.org) is written by Hutch researchers and staff, and is a great place to find information about data management, bioinformatics, computing, and more.

###### tags: `fredhutch.io` `python`