Bootcamp / Session 2 / 2.2
Session 2.2 · Ming “Tommy” Tang, AstraZeneca
Master six plots and you can make most figures.
Six plot types carry about ninety percent of the figures in a genomics paper. This part walks through each one: what it shows, when to reach for it, how to read someone else's, and the ways each can mislead you.
Recording
The six
| Plot | What it shows |
|---|---|
| Barplot | A value per category. The one most often used where a distribution belongs. |
| Scatter plot | Two measurements per point, and the relationship between them. |
| Line graph | Something measured along an ordered axis, usually time or dose. |
| Histogram | The shape of one distribution, including the tails a summary statistic hides. |
| Boxplot and violin | Distributions side by side across groups. |
| Heatmap | A matrix of values, with clustering and annotations on the margins. |
Also in this part
- What the fancy plots are underneath. A clustered dot plot, a volcano, a UMAP panel: each is one of the six with extra encoding layered on.
- Two figures read live. One from a published paper and one from a recent Nature study, taken apart to see what the authors chose and what they left out.
- How a plot misleads. Bars hiding a distribution, axes that do not start at zero, and overplotting that turns thousands of points into a solid blob.
Materials
SlidesSix types of plotsTommy's deck for this part. Work in progress.docs.google.com
ReferenceDirectory of visualizationsClaus Wilke. A named picture of every chart type, and what each is for.clauswilke.com/dataviz
Referenceggplot2 cheatsheetThe grammar, one page, for building these plots in R.github.com/rstudio/cheatsheets
ReferenceComplexHeatmap: annotationsFor heatmaps with sample and gene annotations on the margins.jokergoo.github.io
ReadingClustered dot plot for single-cell RNA-seqTommy's walkthrough of what that plot is made of.divingintogeneticsandgenomics.com
VideoChatomics on YouTubeTommy's channel, including the plotting walkthroughs.youtube.com/@chatomics
After the session
Two minutes of feedback, so the next session is pitched better. It also records your attendance, so fill it in whether you were in the room, on Zoom, or catching up on the recording.