A.9: Jupyter notebook
- Page ID
- 49898
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Jupyter notebook, python. A “web-based computational environment”
Project homepage: https://jupyter.org/
Besides the python kernel, Jupyter kernels include
Cytoscape
SageMATH
and, of course R, which along with python and Julia, is one of the core programming languages available in Jupyter. We present how to install the IRkernel on this page.
In the cloud
Access to Jupyter notebook was discussed for running R in the cloud.
Local installation
# install latest python 3.12.4
# https://www.python.org/
# https://www.python.org/downloads/windows/
# macOS universal installer
# https://www.python.org/downloads/macos/
# default python on macOS
# see how to bash alias at https://stackoverflow.com/questions/...to-3-x-on-os-x
# Open terminal
python3 –version
python3 -m pip –version
# pip3 install jupyterlab
pip install jupyterlab
jupyter lab
browser opens http://localhost:8888/lab
Install IRkernel from CRAN
# Run R in terminal as administrator
sudo R
# At R prompt enter
install.packages(“IRkernel”)
# Making the kernel available to Jupyter
IRkernel::installspec(user = FALSE)
Run R as Jupyter Notebook
In the terminal, type at the bash shell line
jupyter lab
Set working drive, then load kernel. Select the R kernel and create a new Notebook, Figure \(\PageIndex{2}\) (i.e., don’t select a Console).
You should be ready to go.
It’s easy to switch kernels. Let’s say you started Jupyter Lab and notice that Python is running (Fig. \(\PageIndex{5}\)). Click on the kernel name — see green arrow in Figure \(\PageIndex{5}\) — to bring up a popup menu, Fig \(\PageIndex{6}\).
Click on the drop arrow and select R kernel (figure \(\PageIndex{7}\)), then click on blue Select button.
Once you select the R kernel from the dropdown, the kernel should be been successfully switched, as shown in Figure \(\PageIndex{8}\).
