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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.