Lecture4_my-script-with-R_hclust

Jimmy（jmzeng1314@outlook.com）

Keywords: hclust

x=runif(10)

y=runif(10)

S=cbind(x,y) #得到2维的数组

rownames(S)=paste("Name",1:10,"") #赋予名称，便于识别分类

out.dist=dist(S,method="euclidean") #数值变距离

plclust(out.hclust)

rect.hclust(out.hclust,k=3)

out.id=cutree(out.hclust,k=3)

a=read.table("GSE62254_series_matrix.txt.gz",comment.char = "!",stringsAsFactors=F,header=T)

rownames(a)=a[,1]

a=a[,-1]

#> dim(a)

#[1] 54675 300

d=a

mads=apply(d,1,mad)

d=d[rev(order(mads))[1:5000],]

d = sweep(d,1, apply(d,1,median,na.rm=T))

t_d=t(d)

hc <- hclust(dist(t_d), "ave")

png("hclust.png")

plot(hc)

dev.off()