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带有显著性标记的相关性热图绘制方法
参考文献:
https://www.jianshu.com/p/d86ddf8fd48f
https://mp.weixin.qq.com/s/5tHE5apk2SwDmcSLYQx48Q
#psych包用于计算相关性、p值等信息
library(psych)
#pheatmap包用于绘制相关性热图
library(pheatmap)
#reshape2包用于输出数据的整合处理
library(reshape2)
#准备数据
#读取数据
plant=read.table("20200721--Plant.txt", header = T, row.names = 1)
lefse=read.table("20200721--Lefse.txt", header = T, row.names = 1)
#计算相关性
cor = corr.test(lefse, plant, method="spearman", adjust="none")
#提取相关性、p值
cmt <-cor$r
pmt <- cor$p
#判断显著性
if (!is.null(pmt)){
ssmt <- pmt< 0.01
pmt[ssmt] <-'**'
smt <- pmt >0.01& pmt <0.05
pmt[smt] <- '*'
pmt[!ssmt&!smt]<- ''
} else {
pmt <- F
}
#自定义颜色范围
mycol<-colorRampPalette(c("blue","white","tomato"))(800)
#可视化
pheatmap(cmt,scale = "none", cluster_row = F, cluster_col = F, border=NA, fontsize_row=8, fontsize_col=8, display_numbers = pmt, fontsize_number = 10, number_color = "white", cellwidth = 13, cellheight =13,color=mycol, filename="plant.lefse.jpg")
#结果展示
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