使用pheatmap绘制热图

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install.package("pheatmap")
library(pheatmap)

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setwd("path/to/my/workdir/")
data <- read.delim("mydata.txt", header = T, sep = "\t", row.names = 1)

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pheatmap(as.matrix(data), color=colorRampPalette(c("green","black","red"))(100), scale='row', border_color=NA, width=9, height=18, fontsize=9, fontsize_row=6, filename="heatmap.pdf" )

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scale='row' #对矩阵进行标准化，以row或column方向进行标准化，默认参数为none
cluster_row, cluster_col #默认对行列方向均进行聚类，设置为FALSE可不进行相应方向的聚类
treeheight_row=0, treeheight_col=0 #不显示dendrogram
border_color=NA #热图的每个小块间默认以灰色隔开，设置NA去掉border
legend=FALSE #不显示legend
color=colorRampPalette(rev(c("red","black","green")))(102) #设定cell的颜色

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pheatmap(test, display_numbers = TRUE, number_format = "%.2f", number_color="purple") #"%.2f"表示保留小数点后两位
# 在热图格子中展示文本
pheatmap(test, display_numbers = TRUE)
pheatmap(test, display_numbers = TRUE, number_format = "\%.1e")
pheatmap(test, display_numbers = matrix(ifelse(test > 5, "*", ""), nrow(test)))#还可以自己设定要显示的内容

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#pheatmap还可以显示行或列的分组信息，支持多种分组；
annotation_col = data.frame(CellType = factor(rep(c("CT1", "CT2"), 5)), Time = 1:5)
rownames(annotation_col) = paste("Test", 1:10, sep = "")
 
annotation_row = data.frame(GeneClass = factor(rep(c("Path1", "Path2", "Path3"), c(10, 4, 6))))
rownames(annotation_row) = paste("Gene", 1:20, sep = "")
 
pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row)

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#设定各个分组的颜色
ann_colors = list(Time = c("white", "firebrick"), #连续数值型分组可设置成渐变
    CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
    GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E"))
pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row,
         annotation_colors = ann_colors)

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#还可以自己设定各个分组的颜色
ann_colors = list(Time = c("white", "firebrick"), #连续数值型分组可设置成渐变
    CellType = c(CT1 = "#1B9E77", CT2 = "#D95F02"),
    GeneClass = c(Path1 = "#7570B3", Path2 = "#E7298A", Path3 = "#66A61E"))
pheatmap(test, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = ann_colors)
#还可以利用gaps_row, gaps_col自己设定要分隔开的位置
pheatmap(test, annotation_col = annotation_col, cluster_rows = FALSE, gaps_row = c(10, 14), cutree_col = 2)

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#breaks
bk <- c(seq(-9,-0.1,by=0.01),seq(0,9,by=0.01))
#pheatmap
pheatmap(data1,
         scale = "none",
         color = c(colorRampPalette(colors = c("blue","white"))(length(bk)/2),colorRampPalette(colors = c("white","red"))(length(bk)/2)),
         legend_breaks=seq(-8,8,2),
         breaks=bk)