Visualization

plot 10x scATAC coverage by cluster/group

This post was inspired by Andrew Hill’s recent blog post. Inspired by some nice posts by @timoast and @tangming2005 and work from @10xGenomics. Would still definitely have to split BAM files for other tasks, so easy to use tools for that are super useful too! — Andrew J Hill (@ahill_tweets) April 13, 2019 Andrew wrote that blog post in light of my other recent blog post and Tim’s (developer of the almighty Seurat package) blog post.

A tale of two heatmap functions

You probably do not understand heatmap! Please read You probably don’t understand heatmaps by Mick Watson In the blog post, Mick used heatmap function in the stats package, I will try to walk you through comparing heatmap, and heatmap.2 from gplots package. Before I start, I want to quote this: “The defaults of almost every heat map function in R does the hierarchical clustering first, then scales the rows then displays the image”