使用Pheatmap包绘制差异miRNA热图

说明：
测序报告中，生物公司给出的Excel文件，可以将excel另存为csv格式，便于后续分析，当然也可以安装可以直接导入excel文件的R包。

# 清除当前环境中的变量
rm(list=ls())
#设置工作路径
setwd("c:/Users/Administrator/Documents/data_analysis/2018-10-06J.F.XIE_sequencing_data/")
#载入csv文件
sign.miRNA <- read.csv("The total different expression miRNA.csv",header = TRUE)
#将'name列'当作行名
rownames(sign.miRNA) <- sign.miRNA$name
#载入用到的pheatmmap包
library(pheatmap)
#使用csv文档中的第26到37列数据（12列）
>pheatmap(sign.miRNA[,c(26:37)])

Rplot-01.png

#取log2
>pheatmap(log2(sign.miRNA[,c(26:37)]+1))

Rplot-02.png

pheatmap参数调整:
添加标题：main = "total different expression miRNA"
更改色彩搭配： color = colorRampPalette(c("navy","white","firebrick3"))(256)
设置字体大小：fontsize = 9
设定每个热图格子的边框色：border_color = "grey60"
设定行和列聚类树的高度，默认为50：treeheight_row = 20, treeheight_col =20
热图格子大小设置：cellwidth = 8, cellheight = 8
取消按行聚类：cluster_rows = FALSE
参数对行进行归一化：scale = "row"
将列聚类分为4组：cutree_cols = 4

#绘制热图
> pheatmap(log2(sign.miRNA[,c(26:37)]+1),
+          color = colorRampPalette(c("navy","white","firebrick3"))(256),
+          scale = "row", fontsize = 8, border_color = "grey60",
+          treeheight_row = 20, treeheight_col =20,
+          cellwidth = 8, cellheight = 8, cutree_cols = 4)

Rplot-03.png
构建列注释信息

 # 构建列注释信息
> annotation_col = data.frame(
+   Nutrition = factor(rep(c("Sugar","Yeast"), each = 6,len=12)),
+   Microbiota  = factor(rep(c("CON", "AXN"), each = 3, len = 12)))
#为注释信息添加行名
> rownames(annotation_col) = c("Sugar_1","Sugar_2","Sugar_3","Sugar_A1","Sugar_A2","Sugar_A3",
+                              "Yeast_1","Yeast_2","Yeast_3","Yeast_A1","Yeast_A2","Yeast_A3")
#查看添加注释信息
> head(annotation_col)
         Nutrition Microbiota
Sugar_1      Sugar        CON
Sugar_2      Sugar        CON
Sugar_3      Sugar        CON
Sugar_A1     Sugar        AXN
Sugar_A2     Sugar        AXN
Sugar_A3     Sugar        AXN

 #添加注释信息：annotation_col = annotation_col,
 #绘制热图
> pheatmap(log2(sign.miRNA[,c(26:37)]+1),
+          annotation_col = annotation_col,
+          color = colorRampPalette(c("navy","white","firebrick3"))(256),
+          scale = "row", fontsize = 8, border_color = "grey60",
+          treeheight_row = 20, treeheight_col =20,
+          cellwidth = 8, cellheight = 8, cutree_cols = 4)

Rplot-04.png

> pheatmap(log2(sign.miRNA[,c(26:37)]+1),
+          annotation_col = annotation_col,cluster_rows = FALSE,
+          color = colorRampPalette(c("navy","white","firebrick3"))(256),
+          scale = "row", fontsize = 8, border_color = "grey60",
+          treeheight_row = 20, treeheight_col =10,
+          cellwidth = 8, cellheight = 8, cutree_cols = 4, gaps_row = c(30,50))

Rplot-05.png
参考资料1：使用pheatmap包绘制热
参考资料2：热图最佳实践-pheatmap