2020-12-10

com2 <- read.table(file = "C:/Users/vic/Desktop/4_expressions/PanCancerImmune_743.txt", skip = 0, header = TRUE, sep = "\t")

class(com2)
[1] "data.frame"
row.names(com2)
[1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10"
[11] "11" "12" "13" "14" "15" "16" "17" "18" "19" "20"
[21] "21" "22" "23" "24" "25" "26" "27" "28" "29" "30"
[31] "31" "32" "33" "34" "35" "36" "37" "38" "39" "40"
[41] "41" "42" "43" "44" "45" "46" "47" "48" "49" "50"
com2 <- com2[!duplicated(com2[,1]),] #必须先去重再设置rownames
row.names(com2) <- com2$锘縢ene_short_name
View(com2)
dim(com2)
[1] 741 7
com2 <- com2[,2:7]
View(com2)
M=cor(log(com2+1))
pheatmap::pheatmap(scale(M))

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library(pheatmap)
library(stringr)
ac=data.frame(group=str_split(colnames(n),'_',simplify = T)[,1])
rownames(ac)=colnames(n)

pheatmap::pheatmap(n,

•                show_colnames = F,#是否显示列名
  

•                show_rownames = F,
  

•                annotation_col=ac)#增加分组的栏#
  

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当 cg=names(tail(sort(apply(com2,1,sd)),500))时，

ead(cg)
n=com2[cg,]
head(n)

library(pheatmap)
library(stringr)
ac=data.frame(group=str_split(colnames(n),'_',simplify = T)[,1])
rownames(ac)=colnames(n)
pheatmap::pheatmap(n,
show_colnames = F,#是否显示列名
show_rownames = F,
annotation_col=ac,#增加分组的栏
scale = "row")#横的比较wnames(ac)=colnames(n)

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最终敲定

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