How to deal with overplotting without being fooled

Sign up for my newsletter to not miss a post like this The problem Let me be clear, when you have gazillions of data points in a scatter plot, you want to deal with the overplotting to avoid drawing misleading conclusions. Let’s start with a single-cell example. Load the libraries: library(dplyr) library(Seurat) library(patchwork) library(ggplot2) library(ComplexHeatmap) library(SeuratData) set.seed(1234) prepare the data data("pbmc3k") pbmc3k #> An object of class Seurat #> 13714 features across 2700 samples within 1 assay #> Active assay: RNA (13714 features, 0 variable features) ## routine processing pbmc3k<- pbmc3k %>% NormalizeData(normalization.