How to deal with overplotting without being fooled

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