Welcome

Bioconductor Sticker

One of the most important parts of single-cell data analysis is visualization. In fact, it could even be said that this is the most important part of the analysis. How else can we make Figure 1 of our Nature papers without some sweet, sweet \(t\)-SNEs? (Or UMAPs.) We need something to compete with the aesthetic appeal of a “representative” microscope image, after all.

This book will showcase various methods for visualizing single-cell data from a SingleCellExperiment object. Each chapter focuses on a particular aspect of data visualization, starting with a brief analysis to set up the SingleCellExperiment before applying a range of plotting functions. Readers can then pick and choose their poison in a bake-off between visualization philosophies.

All of the visualization packages presented here are available from the Bioconductor project. The major players are scater, a trusty old workhorse for working with SingleCellExperiment objects; dittoSeq, a more recent package focusing on colorblind-friendly visualizations; and scDataviz, yet another upstart offering plotting capabilities. If you’re a Bioconductor package developer and you think you can do better, bring it. (With a PR.)

I’ll finish with a quote from Keats, for those of us unfortunate enough to have study poetry in high school:

“Beauty is truth, truth beauty,”–that is all Ye know on earth, and all ye need to know.

Pretty much sums up the field.