Heatmap

Dotplots are very popular for visualizing single-cell RNAseq data. In essence, the dot size represents the percentage of cells that are positive for that gene; the color intensity represents the average gene expression of that gene in a cell type. It is easy to plot one using Seurat::dotplot or Sccustomize::clustered_dotplot. However, when you have multiple groups/conditions in your data and you want to visualize it by groups, it is not that straightforward.

In this blog post, I am going to show you how to make a correlation heatmap with p-values and significant values labeled in the heatmap body. Let’s use the PBMC single cell data as an example. You may want to read my previous blog post How to do gene correlation for single-cell RNAseq data. Load libraries library(dplyr) library(Seurat) library(patchwork) library(ggplot2) library(ComplexHeatmap) library(SeuratData) library(hdWGCNA) library(WGCNA) 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.

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”