SISBID 2026 Module 2: Data Visualization

Instructors: Di Cook, Heike Hofmann and Susan Vanderplas

Website: https://dicook.github.io/SISBID/

Module description

We will present general-purpose techniques for visualizing a variety of data, as well as specific techniques for visualizing common types of biological data sets. Some strategies for working with large data will be provided. Understanding data involves an iterative cycle of visualization and modeling. We will illustrate this with several examples during the workshop.

The first segment of this module will focus on structured development of graphics using static graphics. This will use the ggplot2 package in R. It enables building plots using grammatically defined elements, and producing templates for use with multiple data sets. We will include some these principles for working with biological and genomic data.

The second segment will focus on interactive graphics for rapid exploration. We will also demonstrate interactive techniques for high-performance local display, and for easily creating interactive web graphics. In addition, we will explain how to create simple web GUIs for managing interactive analysis tools for data using shiny.

We will use a hands-on teaching methodology that combines short lectures with longer practice sessions. As students learn about new techniques, they will also be able to put them into practice and receive feedback from experts.

Module assumes some familiarity with R. We will teach using R and Rstudio.

Course Logistics

We use zoom for lectures. All sessions will be recorded and made available.

Communication with the instructors should be in Zoom or on the slack channel.

Zoom etiquette:

mute yourself when not talking,
don’t share the link.

Course Schedule

Monday	US Pacific	US Central	US Eastern	Accra	London	Korea	Melbourne
Meet & Greet	7:45 - 8:00 am	9:45 - 10:00 am	10:45 - 11:00 am	2:45 - 3:00 pm	3:45 - 4:00 pm	11:45 am - 12:00 pm	12:45 - 1:00 am
Lecture 1	8:00 - 8:45 am	10:00 - 10:45 am	11:00 - 11:45 am	3:00 - 3:45 pm	4:00 - 4:45 pm	12:00 - 12:45 am	1:00 - 1:45 am
Lecture 2	9:00 - 9:45 am	11:00 - 11:45 am	12:00 - 12:45 pm	4:00 - 4:45 pm	5:00 - 5:45 pm	1:00 - 1:45 am	2:00 - 2:45 am
Lecture 3	10:00 - 10:45 am	12:00 - 12:45 pm	1:00 - 1:45 pm	5:00 - 5:45 pm	6:00 - 6:45 pm	2:00 - 2:45 am	3:00 - 3:45 am
Break
Lecture 4	11:45 - 12:30	1:45 - 2:30 pm	2:45 - 3:30 pm	6:45 - 7:30 pm	7:45 - 8:30 pm	3:45 - 4:30 am	4:45 - 5:30 pm
Lecture 5	12:45 - 1:30 pm	2:45 - 3:30 pm	3:45 - 4:30 pm	7:45 - 8:30 pm	8:45 - 9:30 pm	4:45 - 5:30 am	5:45 - 6:30 am
Lecture 6	1:45 - 2:30 pm	3:45 - 4:30 pm	4:45 - 5:30 pm	8:45 - 9:30 pm	9:45 - 10:30 pm	5:45 - 6:30 am	6:45 - 7:30 am

Tuesday	US Pacific	US Central	US Eastern	Accra	London	Korea	Melbourne
Lecture 7	8:00 - 8:45 am	10:00 - 10:45 am	11:00 - 11:45 am	3:00 - 3:45 pm	4:00 - 4:45 pm	12:00 - 12:45 am	1:00 - 1:45 am
Lecture 8	9:00 - 9:45 am	11:00 - 11:45 am	12:00 - 12:45 pm	4:00 - 4:45 pm	5:00 - 5:45 pm	1:00 - 1:45 am	2:00 - 2:45 am
Lecture 9	10:00 - 10:45 am	12:00 - 12:45 pm	1:00 - 1:45 pm	5:00 - 5:45 pm	6:00 - 6:45 pm	2:00 - 2:45 am	3:00 - 3:45 am
Break
Lecture 10	11:45 - 12:30	1:45 - 2:30 pm	2:45 - 3:30 pm	6:45 - 7:30 pm	7:45 - 8:30 pm	3:45 - 4:30 am	4:45 - 5:30 pm
Lecture 11	12:45 - 1:30 pm	2:45 - 3:30 pm	3:45 - 4:30 pm	7:45 - 8:30 pm	8:45 - 9:30 pm	4:45 - 5:30 am	5:45 - 6:30 am
Lecture 12	1:45 - 2:30 pm	3:45 - 4:30 pm	4:45 - 5:30 pm	8:45 - 9:30 pm	9:45 - 10:30 pm	5:45 - 6:30 am	6:45 - 7:30 am

Wednesday	US Pacific	US Central	US Eastern	Accra	London	Korea	Melbourne
Lecture 13	8:00 - 8:45 am	10:00 - 10:45 am	11:00 - 11:45 am	3:00 - 3:45 pm	4:00 - 4:45 pm	12:00 - 12:45 am	1:00 - 1:45 am
Lecture 14	9:00 - 9:45 am	11:00 - 11:45 am	12:00 - 12:45 pm	4:00 - 4:45 pm	5:00 - 5:45 pm	1:00 - 1:45 am	2:00 - 2:45 am
Lecture 15 / Show and Tell	10:00 - 10:45 am	12:00 - 12:45 pm	1:00 - 1:45 pm	5:00 - 5:45 pm	6:00 - 6:45 pm	2:00 - 2:45 am	3:00 - 3:45 am

Course outline

Slack

Find us on slack: SISBID.slack.com. The channel data-visualization-2026 will contain zoom and (later) video links for the sessions.

Monday

Day 1 zip file

Title	Slides	1pg Slides	Code	Instructor
0. Setting things up	Slides	1pg	Code	All
1. The grammar of graphics and ggplot2	Slides	1pg	Code	Heike
2. Visual perception and effective plot construction	Slides	1pg	Code	Susan
3. Tidy data and tidying messy data with tidyr	Slides	1pg	Code	Heike
Break
4. Reshaping Data for Plotting and Display	Slides	1pg	Code	Susan
5. Wrangling data and models	Slides	1pg	Code	Heike
6. Advancing the grammar to maps, time and interactivity	Slides	1pg	Code	Di

Tuesday

Day 2 zip file
Note: this zip file assumes you will extract to the same folder as yesterday – data files have not been included twice.

Title	Slides	1pg Slides	Code	Instructor
7. Interactive and animated graphics using plotly and gganimate	Slides	1pg	Code	Heike
8. How to build a shiny app	Slides	1pg	Code	Heike
9. Reactive elements in shiny	Slides	1pg	Code	Susan
Break
10. Multivariate plots using ggplot2, GGally	Slides	1pg	Code	Di
11. Touring on multivariate data	Slides	1pg	Code	Di
12. Advanced graphics and statistical inference	Slides	1pg	Code	Di

Wednesday

Day 3 zip file
Note: this zip file assumes you will extract to the same folder as Monday – data files have not been included twice.

Title	Slides	1pg Slides	Code	Instructor
13. Theme a shiny app	Slides	1pg	Code	Susan
14. Build your own Shiny app	Slides	1pg	Code	Heike
Show us What You’ve Made				All
15. Interactive Documents	Slides	1pg	Code	Susan

Software list

Download RStudio, and latest R version.

Open RStudio, and run the code below to install these packages and their dependencies:

# CRAN packages
packages <- c(
  "here", "readr", "readxl", "splitstackshape", "tidyr", "dplyr", "lubridate",
  "stringr", "purrr", "ggplot2", "ggthemes", "RColorBrewer", "scales",
  "dichromat", "colorspace", "viridis", "ggbeeswarm", "ggmap", "gridExtra",
  "GGally", "ggpcp", "corrgram", "tourr", "gganimate", "maps","datasauRus",
  "gapminder", "cranlogs", "shiny", "bslib", "DT", "leaflet", "plotly",
  "htmltools", "broom", "broom.mixed", "lme4", "MASS", "forecast", "nullabor",
  "ggdist", "bsicons", "ragg", "showtext", "thematic", "remotes", "quarto",
  "bslib")

# Install packages and their dependencies
to_install <- setdiff(packages, installed.packages())
install.packages(to_install, dep=TRUE, repos = "https://cloud.r-project.org/")

# Install some packages from GitHub
# If you can't install these,
# it won't affect your ability to participate
remotes::install_github("wmurphyrd/fiftystater")
remotes::install_github("heike/vinference")
remotes::install_github("rstudio/bslib")
remotes::install_github("rlbarter/superheat")

# For sharing web apps,
# but you need administrator rights to your computer:
install.packages("rsconnect")

Note: You can install all of the tidyverse of packages - tidyr, dplyr, readr, ggplot2, tibble, purrr, forcats, stringr - with install.packages("tidyverse"). But some operating systems seem to run into difficulties doing this, so installing just a subset is easier.

If you want to compile the slides - you really don’t want to do this, but if you do - you will need these additional packages:

install.packages("remotes")
remotes::install_github("hadley/emo")
remotes::install_github("mitchelloharawild/icons")
remotes::install_github("emitanaka/anicon")
remotes::install_github("dicook/gretchenalbrecht")
remotes::install_github("gadenbuie/countdown", subdir = "r")
install.packages("xaringanExtra")