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.
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.