这里依然需要一张meme
前后文和数据来源见 『生信技能树』R语言20题之我的答案版本 第13题。
1. pheatmap
> top50gene=tail(sort(madlist),50)
> top50gene=as.data.frame(top50gene)
> top50genelist=rownames(top50gene)
> top50matrix=uni_e[top50genelist,]
> ct=scale(top50matrix,center=T,scale=F) ## 中心化
> nmlztop50matrix=scale(ct,center=T,scale=T) ## 标准化
> pheatmap::pheatmap(nmlztop50matrix)
2. heatmap
> heatmap(nmlztop50matrix)
3. ggplot
> ggplot(ml_nmtop50,aes(sample,symbol))+
+ geom_tile(aes(fill=value),colour = "white")+
+ scale_fill_gradient(low = "white",high = "steelblue")
4. gplots
> library(gplots)
> heatmap.2(nmlztop50matrix,key = T,symkey = FALSE,density.info="none",trace="none")
5. lattice, latticeExtra
> library(lattice)
> library(latticeExtra)
> x <- t(as.matrix(scale(nmlztop50matrix)))
> dd.row <- as.dendrogram(hclust(dist(x)))
> row.ord <- order.dendrogram(dd.row)
> levelplot(t(nmlztop50matrix),aspect = "fill",xlab="sample",ylab="symbol",colorkey = list(space = "left"),legend=list(right=list(fun=dendrogramGrob,args=list(x=dd.row,rod=row.ord,side='right',size=5))))
> levelplot(t(nmlztop50matrix),aspect =
+ "fill",xlab="sample",ylab="symbol",colorkey =
+ list(space = "left"),legend=
+ list(right=list(fun=dendrogramGrob,args=
+ list(x=dd.row,rod=row.ord,side='right',size=5))))
