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How to: Jupyter

Table of content / internal links

In table of content:

[loading data](#loading)
  • To add space character at the beginning of item 
      # repeat the command for more spaces

In text:

<a name="loading"></a>

Auto reload

# Make sure there are no empty spaces at the end of the lines 
%load_ext autoreload
%autoreload 2

Create kernel

To create a new kernel:

pip install ipykernel  
ipython kernel install --user --name=projectname

Select the new kernel from the notebook (top-right)

Uninstall kernel

To delete a kernel

jupyter kernelspec list  # to get the paths of all your kernels  
jupyter kernelspec uninstall unwanted-kernel-name # to uninstall your unwanted-kernel-name

Installing widgets

pip install ipywidgets
jupyter nbextension enable --py widgetsnbextension

# for jupyter lab
jupyter labextension install @jupyter-widgets/jupyterlab-manager  

# make sure the following are updated
jupyter labextension install @pyviz/jupyterlab_pyviz
jupyter labextension install @jupyterlab/toc

Restart JupyterLab if it the visualization does not occur

itkwidget

pip install itkwidgets
jupyter labextension install @jupyter-widgets/jupyterlab-manager itk-jupyter-widgets

Mixing python and R

Prerequisites (on Mac)

  • Install last python
  • Install last R 3.3.3
    (Note on Dec 11, 2018: the older versions of R are compiled with gcc instead of clang, so pip install rpy2 does not work. To install rpy2 with R > 3.3.3, one has to install the gcc compiler with conda install llvm gcc libgcc1. However this downgrades python to 2.7, which means that commands like autoreload in Jupyter do not work anymore)
  • In terminal:
    • Install rpy2 
      pip install rpy2
      (it might uninstall some packages - just reinstall them)
  • Get R path: 
    R HOME #to get R home (e.g. /Library/Frameworks/R.framework/Resources)

In notebook

import os
os.environ['R_HOME'] = '/Library/Frameworks/R.framework/Resources'
%load_ext rpy2.ipython

# example:
# python's pandas dataframe
import pandas as pd
df = pd.DataFrame({
    "cups_of_coffee": [0,1,2,3,4,5,6,7,8,9],
    "productivity": [2,5,6,8,9,8,0,1,0,-1]
})
# R's ggplot2
%%R -i df -w 5 -h 5 --units in -r 200
# import df from global environment
# make default figure size 5 by 5 inches with 200 dpi resolution

# install.packages("ggplot2", repos='http://cran.us.r-project.org', quiet=TRUE) (#uncomment the first time)
library(ggplot2)
ggplot(df, aes(x=cups_of_coffee, y=productivity)) + geom_line()

Markdown

  • Change font color: 
    <font color='blue'>