Under the hood, this
1) gets the avg (pseudobulk) gene expression of each type,
2) computes the similarity matrix,
3) projects expression into a 3D space using MDS, and
4) interprets the space as a perceptually uniform color space (LUV)

Good scientific plotting uses color to convey meaning. We don't want to distract readers. Yet with default categorical maps,

(-) some cell types jump out for no reason
(-) perceptual similarity between colors is meaningless
(-) fewer colors than types, leading to repeats

Do you plot transcriptomic data, coloring each cell by its cell type? ~ Don't use a default colormap! ~

Instead, use colormaps that capture biological meaning. If two cell types are very similar, their colors should be similar too. Read on 🧵

🧬💻

TIL that Earth and the inner planets don't have stable orbits. Their eccentricities evolve chaotically, and by a lot. In about 1% of simulations, inner planets collide with each other in the next few billion years

www.scholarpedia.org/article/Stab...

seeing these two crabs literally changes your brain