RNA-seq聚类图

标准化方法
RNA-seq多Run合并、VST标准化、PCA、差异分析
最全的R语言聚类树形图画法
我的一个例子

rm(list=ls())
suppressMessages(library(DESeq2))
suppressMessages(library(RColorBrewer))
suppressMessages(library(ggplot2))
suppressMessages(library(ggrepel))
suppressMessages(library(ape))
counts_data_counts<-read.csv(paste0(your_dir,"/counts_data_common_counts.csv"),header = T,row.names = 1)
coldata<-read.csv(paste0(your_dir,"/counts_data_common_group.csv"),header = T,row.names = 1)
data<-counts_data_counts[,row.names(coldata)]
ddsOrig <- DESeqDataSetFromMatrix(countData=data, colData=coldata, 
                                  design=~group + condition)
suppressMessages(ddsOrig <- DESeq(ddsOrig))
rld <- rlogTransformation(ddsOrig)
exprSet_new<-assay(rld)
hc = hclust(dist(t(exprSet_new)))
p<-plot(as.phylo(hc), type = "fan")
plot(p)