首先准备数据：
| gene_id | id |
TCGA-2J-AAB101A-11R-A41B-07 |
TCGA-2J-AAB4-01A-12R-A41B-07 | TCGA-2J-AAB6-01A-11R-A41B-07 | TCGA-2J-AAB8-01A-12R-A41B-07 | TCGA-2J-AAB9-01A-11R-A41B-07 | TCGA-2J-AABA-01A-21R-A41B-07 |
| APLP2 | 334 | 20091.2 | 23546.3 | 18321.6 | 14173.4 | 18687 | 18471.9 |
| OLR1 | 4973 | 397.561 | 925.084 | 766.082 | 585.664 | 755.627 | 177.861 |
| PLXDC1 | 57125 | 797.507 | 600.088 | 628.012 | 744.536 | 849.946 | 421.425 |
| SEMA3C | 10512 | 965.366 | 797.98 | 5651.46 | 1521.03 | 2662.38 | 3890.4 |
用R绘制热图：首先要安装pheatmap包
install.packages("pheatmap")
然后根据表达量绘制，横轴作为样本（分为两组），纵轴作为基因。
1.导入数据data <- read.table("gene.txt",header = T)
data_2 <- data[-1,-c(1,2)] ＃只保留表达值 data_2<-apply(data_2,2, as.numeric) ＃将其转换为数值型，有时候你的数据可能是经过不同格式转换过来的，需要注意 as.numeric(data_2) data_3 <- matrix(as.numeric(data_2),nrow = nrow(data_2)) ＃制作矩阵 rownames(data_3)<-data[-1,]$gene_id ＃添加行名基因 colnames(data_3)<-colnames(data_2) ＃添加列名样本 data_3[data_3 <= 0] = 0.0001 data_3[1:4,1:4]
2. log数据
logData = apply(data_3, 2, log2)
3. 用preprocessCore包做标准化，此步骤在你不需要的时候可以省略
library("preprocessCore")
logData = normalize.quantiles(logData)
rownames(logData) = rownames(data_3)
colnames(logData) = colnames(data_3)
boxplot(logData)
4. 热图，用heatmap
group<-factor(c(rep(‘group1‘,22),rep(‘group2‘,23))) #分组
patientcolors = c("green","red")[group] #将两组分别标记为红色和绿色
##logData[logData<= "-lnf"] = -3
heatmap(logData, col = colorRampPalette ( rev ( c ( "red" , "white" , "green" ) ) ) ( 102 ),Colv=NA, ColSideColors=patientcolors, cexRow=0.5)
5. 热图，用pheatmap
library(pheatmap)
annotation = data.frame(Class=group)
rownames(annotation) = colnames(logData)
pheatmap( logData, annotation=annotation, color = colorRampPalette(c("darkgreen", "gray99", "red"))(500), cellwidth = 10, cellheight = 3,scale="row", cluster_rows = TRUE,
cluster_cols = FALSE, show_rownames=T, show_colnames=T, fontsize=8, fontsize_col=6,fontsize_row=3, border_color= NA,filename = "test.pdf")
具体的修改，大家可以参见其参数设置。
https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf
原文：http://www.cnblogs.com/qiniqnyang/p/6349384.html