heatmap.R

rm(list=ls())#clear Global Environment
setwd("C:/Users/Harry/Downloads/热图")

#加载R包
library (pheatmap)
#读取数据
df <- read.table(file="data11.txt",sep="\t",row.names = 1, header=T,check.names=FALSE)
#查看前3行
head(df)[1:5,]

##          A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T
## Rasa2   30 42 36  2 43  5 29 49 33 86 76 86 95 80 73 67 96 81 69 77
## Mmp16   17 47  6 45 32 29 46 46  5 69 65 51 50 80 95 58 85 52 96 70
## Ptar1   34  7 31 34  3 10 46 22 25 62 72 72 77 84 77 61 80 92 64 80
## Zbtb37  23 22 34 16 38 35  7 43 16 63 98 93 98 74 67 86 77 71 52 82
## Vmn2r44  9 16 32 40 10 10 26 40  8 71 93 76 93 91 64 68 53 64 63 68

####Z-score转换以保留数据的真实差异
df1 <-df[apply(df,1,var)!=0,]  ##去掉方差为0的行，也就是值全都一致的行
df_zscore <-as.data.frame(t(apply(df1,1,scale)))#标准化数据，获得Z-score
colnames(df_zscore)<- colnames(df)
###初步绘图
pheatmap(df_zscore,
         angle_col = "45", 
         cellwidth=25, cellheight=8, 
         treeheight_col = 15)

#设置颜色
pheatmap(df_zscore,
         angle_col = "45", 
         cellwidth=25, cellheight=8, 
         treeheight_col = 15,
         color=colorRampPalette(c("#3952a2","black","#f5ea14"))(100))

#添加行注释信息
annotation_col<- data.frame( "Treatment" = c("Saline","Saline","Saline","Cocaine","Saline",
                                           "LSD","LSD","LSD","LSD","Saline",
                                           "Saline","Saline","MDMA","MDMA","MDMA",
                                           "Ketamine","Ketamine","Ketamine","Ketamine","Ketamine"),
                            "Batch" = c("1","1","1","1","2",
                                       "1","2","3","2","1",
                                       "2","2","2","1","2",
                                       "1","3","3","3","3"),
                             "Post_treatment" = c("48 h","2 wk","2 wk","48 h","48 h",
                                                "48 h","2 wk","48 h","48 h","2 wk",
                                                "48 h","2 wk","2 wk","2 wk","2 wk",
                                                "2 wk","48 h","48 h","48 h","48 h"),
                            "Critical_period" = c("Closed","Closed","Closed","Closed","Closed",
                                                   "Closed","Closed","Closed","Closed","Open",
                                                   "Open","Open","Open","Open","Open",
                                                   "Open","Open","Open","Open","Open"))#行注释矩阵
rownames(annotation_col) = colnames(df_zscore)
colors  <-  list("Treatment" = c(Saline = "#000000", Cocaine = "#575757",LSD = "#e79600",MDMA="#a42422",Ketamine="#c53a8e"), 
                 "Batch" = c( "1"= "#3953a3", "2" = "#ef4a4a", "3" = "#009848"),
                 "Post_treatment" = c("48 h"="#64838c","2 wk"="#2c3a3e"),
                 "Critical_period" = c(Closed="#94c83d",Open="#4e2469"))
pheatmap(df_zscore,
         angle_col = "45", 
         cellwidth=25, cellheight=8, 
         treeheight_col = 15,
         color=colorRampPalette(c("#3952a2","black","#f5ea14"))(100),
         annotation_col = annotation_col,
         annotation_colors = colors,
         show_colnames = F)

###美化
pheatmap(df_zscore,
         angle_col = "45", 
         cellwidth=25, cellheight=8, 
         treeheight_col = 15,
         color=colorRampPalette(c("#3952a2","black","#f5ea14"))(100),
         annotation_col = annotation_col,
         annotation_colors = colors,
         show_colnames = F,
         fontsize_row=9, fontsize=12,
         labels_row = as.expression(lapply(rownames(df_zscore),function(x) bquote(italic(.(x))))),#行名斜体
         filename = "heatmap.pdf")