Let's Plot 7: Clustered Dot Plots in the ggverse

2020 03 23 Update Intro Example dotplot How do I make a dotplot? But let’s do this ourself! Dotplot! Zero effort Remove dots where there is zero (or near zero expression) Better color, better theme, rotate x axis labels Tweak color scaling Now what? Hey look: ggtree Let’s glue them together with cowplot How do we do better? Two more tweak options if you are having trouble: One more adjust Moonshot Downside Exercises for the reader OLD Solution (kept for posterity) 2020 03 23 Update Ming Tang pointed out a better way to align plots, so I have rewritten the back end of this post.

Seurat FindMarker with Cluster N vs M

What Easy cluster by cluster Seurat FindMarkers implementation Why Because Seurat’s FindMarkers (which can be parallelized if you also load library(Future) and plan("multiprocess")) runs with cluster N against all other clusters. People kept asking me for “well what about cluster 23 vs 17” and I kept saying “uh, I haven’t run that because…” How This is being done a Mac. This may not work on a PC. Multicore stuffs are complicated.