Precourse

These are steps to be completed before the workshop

Installations

R

Download and install the latest version of R from r-project.org.

IDE

Install RStudio or Positron. RStudio/Positron provides you with tools like code editor with highlighting, project management, version control, package building, debugger, profiler and more. Visual Studio code is another good alternative to RStudio/Positron.

Quarto

Download and install the latest version of Quarto from quarto.org.

R packages

Install all the R packages necessary for this course by opening an R terminal either in Rstudio or VScode and pasting the following command:

install.packages(c("cowplot","crosstalk","dplyr","DT","gganimate","ggiraph",
                    "ggplot2","ggpubr","ggrepel","ggthemes","grid","gridExtra",
                    "gt", "kableExtra","leaflet","palmerpenguins","patchwork",
                    "pheatmap","plotly","reshape2","scales","Seurat","shiny",
                    "tidyr","tidyverse","wesanderson"), dependencies = TRUE)
Tip

To make sure that the installations went well, we will try to make a quick plot using the packages you just installed. In this plot, we try to see if there is correlation plot between BMI and average no.of steps taken by some volunteers per day. The data and the code for plotting is available here. Just render or preview the installation_check.qmd file in RStudio or VScode. and you should see the correlation plot, if all the packages are installed properly.

Caution Download course files

Please download all the necessary files from here and make sure that the directory tree looks similar to the one displayed in that page.

HackMD

We will use the online note-keeping document from HackMD for our questions. Please click here to see the notebook. We would appreciate it a lot if you could write your questions and feedback here, so that all participants can learn from each other.

Preparations

To prepare for the course, you can follow one of the links below to warm up your skills necessary for the course.

Tip

Alternative installations with containers

Docker

If you are more familiar with using Docker, all the tools necessary for the course are available as a Docker image. You can pull the image using the following command:

docker pull ghcr.io/nbisweden/workshop-adv-data-viz:latest

If you would like to try to install Docker and give it a try, please follow the instructions here

Visual Studio code

The best and most efficient way to work with the Docker image is with VScode and the extension Dev Containers. Similar to RStudio or Posit, VScode is an IDE maintained by Microsoft and it is quite efficient and robust for all Operating systems.

  • To install VScode, follow the instructions here
  • After successful installation of VScode and Docker, you can install the Dev Containers extension for VScode from here
  • Download the Dev Container file from here Make sure that all the course related files are in the same place as this .devcontainer.json hidden file
  • Then in VScode, press Ctrl+Shift+P (Cmd+Shift+P for Mac users) followed by entering Dev Containers: Open Folder in Container in the prompt to select the folder where you have all the files or Dev Containers: Reopen in Container, if you are already on VScode in the same directory.
  • Now, if everything worked fine, a new window should appear inside the Advanced Data Visualization container.

Apptainer

If for some reason, the installations doesn’t work on your computer and you happened to have access to any of the Swedish HPCs (non-sensitive) like in NAISS. You can follow the instructions below:

In some cases in Dardel HPC from KTH, you might have to load the apptainer module first. The example below explains how one could do it in Dardel.

module load PDC apptainer

Followed by:

apptainer pull workshop.sif ghcr.io/nbisweden/workshop-adv-data-viz:latest
apptainer exec workshop.sif code tunnel

Then follow the on-screen instructions to login with your GitHub account (for example). By following these steps you should have access to all the tools. You can also download all the course files into your HPC at the same location as the workshop.sif file and you should be able to access it in the apptainer. Alternatively, you can also open specific folder in HPC where you have all the workshop related materials from the VS code graphical interface (File --> Open Folder).