加載需要的R包：

library(reshape2)

library(ggplot2)

library(ggtree)? #需要在bioconductor下載

讀入數(shù)據(jù)：

gene <- read.csv(file = "clipboard",header = T,sep = "\t",check.names = F,row.names = 1)

gene

gg <- hclust(dist(gene))? ? #對(duì)行聚類

zz <- hclust(dist(t(gene)))? ? #對(duì)列聚類

gene <- gene[,zz$order]? ? ? #列，按照聚類結(jié)果排序

gene <- gene[gg$order,]? ? ?#行，按照聚類結(jié)果排序

gene <- cbind(name = row.names(gene),gene)

data <- melt(gene,id.vars = "name")? ?#寬數(shù)據(jù)變?yōu)殚L(zhǎng)數(shù)據(jù)

data$num <- rep(c(1:26),6)? ?#繪圖時(shí)的縱坐標(biāo)

data$x <- rep(c(1:6),each = 26)? ?#繪圖時(shí)的橫坐標(biāo)

開始繪圖：

heatmap <- ggplot(data)+

? geom_tile(aes(x = x,y = num,alpha = 0.7),fill = "white",color = "gray")+

? geom_point(aes(x = x,y = num,size = value,color = value),shape = 18)+

? scale_color_gradient2(low = "green",high = "red",mid = "white",midpoint = 6,name = "FPKM",

? ? ? ? ? ? ? ? ? ? ? ? guide = guide_colourbar(barheight = unit(10,"cm"),title.theme = element_text(size = rel(15))))+

? scale_y_discrete(position = c("right"),limits = factor(c(1:26)),label = gene$name)+

? scale_x_discrete(limits = factor(c(1:6)),label = c(colnames(gene)[2:7]))+

? scale_size_continuous(range = c(4,9),guide = NULL)+

? scale_alpha(guide = NULL)+

? labs(x = NULL)+

? theme(panel.background = element_blank(),

? ? ? ? axis.line.x = element_blank(),

? ? ? ? axis.line.y = element_blank(),

? ? ? ? axis.title.y = element_blank(),

? ? ? ? axis.title.x = element_text(size = rel(2),hjust = 0.5),

? ? ? ? axis.text.x = element_text(size = rel(2),hjust = 0.5),

? ? ? ? axis.text.y = element_text(hjust = 0.5,size = rel(2)),

? ? ? ? axis.ticks.x = element_blank(),

? ? ? ? axis.ticks.y = element_blank(),

? ? ? ? plot.title = element_text(size = rel(1.8)),

? ? ? ? plot.margin = margin(15,9,9,30))

繪制聚類樹：

h <- ggtree(gg,layout = "rectangular",branch.length = "none")? # 繪制列聚類樹

v <- ggtree(zz)+layout_dendrogram()? # 繪制行聚類樹

繪制分組信息：

group <- rep(c("A","B"),each = 3) %>% data.frame(x = c(1:6),y = rep(1,6)) %>%

? ggplot()+

? ? geom_tile(aes(x,y,fill = .))+

? ? scale_fill_discrete(label = c("control","treat"))+

? ? theme(panel.background = element_blank(),

? ? ? ? ? axis.line = element_blank(),

? ? ? ? ? axis.title = element_blank(),

? ? ? ? ? axis.text = element_blank(),

? ? ? ? ? axis.ticks = element_blank(),

? ? ? ? ? plot.title = element_blank())

熱圖和聚類樹拼在一起：

heatmap %>% insert_top(group,height = 0.02) %>% insert_top(v,height = 0.1) %>% insert_left(h,width = 0.3)? ?#使用 aplot包里的函數(shù)進(jìn)行拼圖

最終結(jié)果：