之前热图的文档已经写了不少，组内相关性热图，组间相关性热图，ggplot2版热图，ggplot2版圆形热图都有涉及；但是今天来介绍如何通过circlize来绘制高端圆形热图，可以点击下方链接观看之前的文档，后台回复20210926获取本文数据及其代码
ggplot2绘制组内相关性热图
ggplot2绘制组间相关性热图
ggplot2版热图
ggplot2绘制圆形热图
加载R包
library(tidyverse)
library(circlize)
library(stringr)
library(dendextend)
library(ComplexHeatmap)
数据清洗
df <- read_tsv("genes.counts.DESeq2.xls") %>%
mutate(gene_type=if_else(
padj > 0.05,"ns",if_else(
abs(log2FoldChange) < 1,"ns",
if_else(log2FoldChange >=1,"up","down"))),
FC=2**log2FoldChange) %>% filter(gene_type=="up",FC>8) %>%
mutate(across("id",str_replace,"TF","HF")) %>% select(1) %>%
left_join(.,read.delim("genes.TMM.xls") %>%
dplyr::rename(id="X"),by="id") %>%
column_to_rownames("id") %>%
mutate_if(is.numeric,function(x) x+1) %>%
log10() %>% select(1,2,3,4,5,6,7,8,9) %>%
rename_at(vars(starts_with("BLO_")),funs(str_remove(.,"BLO_"))) # 移除BLO_
设置分组
split = sample(letters[1:4],95, replace = TRUE)
split = factor(split, levels = letters[1:4])
定义颜色
col_fun1 = colorRamp2(c(0,1,2,3,4,5),
c("#3B9AB2","#0072B5FF","#E18727FF","#20854EFF","#00A08A","#78B7C5"))
绘制最外圈
circos.par(gap.after=c(1,1,1,20))
circos.heatmap(df[,1:3],col = col_fun1,rownames.side = "outside",split = split,
cluster = T,track.height =0.1)
# 添加样本名称
circos.track(track.index = get.current.track.index(),
panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 4) {
cn = colnames(df1)
n = length(cn)
circos.text(rep(CELL_META$cell.xlim[2],n) + convert_x(0.8,"mm"),
1:n, cn,
cex = 0.5, adj = c(0,0.5),facing = "inside")
}
}, bg.border = NA)
绘制中间圈层
circos.heatmap(df[,4:6],col = col_fun1,cluster = T,track.height =0.1)
circos.track(track.index = get.current.track.index(),
panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 4) {
cn = colnames(df2)
n = length(cn)
circos.text(rep(CELL_META$cell.xlim[2],n) + convert_x(0.8,"mm"),
1:n, cn,
cex = 0.5, adj = c(0,0.5),facing = "inside")
}
}, bg.border = NA)
绘制最内圈
circos.heatmap(df[,7:9],col = col_fun1,cluster = T,track.height =0.1)
circos.track(track.index = get.current.track.index(),
panel.fun = function(x, y) {
if(CELL_META$sector.numeric.index == 4) {
cn = colnames(df3)
n = length(cn)
circos.text(rep(CELL_META$cell.xlim[2],n) + convert_x(0.8,"mm"),
1:n-0.5, cn,
cex = 0.5, adj = c(0,0.5),facing = "inside")
}
}, bg.border = NA)
添加分组名称
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
circos.text(CELL_META$xcenter, CELL_META$cell.ylim[2] + convert_y(34,"mm"),
paste0("group ", CELL_META$sector.index),
facing = "bending.inside", cex = 0.8,
adj = c(0.5, 0), niceFacing = TRUE)
}, bg.border = NA)
添加分组彩带
circos.rect(CELL_META$cell.xlim[2] + convert_x(17, "mm"), 15,
CELL_META$cell.xlim[2] + convert_x(82.5, "mm"), 16,
col = "#3C5488FF", border = NA)
circos.rect(CELL_META$cell.xlim[2] + convert_x(82.5, "mm"), 15,
CELL_META$cell.xlim[2] + convert_x(156.5, "mm"), 16,
col = "#00A087FF", border = NA)
circos.rect(CELL_META$cell.xlim[2] + convert_x(156.5, "mm"), 15,
CELL_META$cell.xlim[2] + convert_x(225.5, "mm"), 16,
col = "#4DBBD5FF",border = NA)
circos.rect(CELL_META$cell.xlim[2] + convert_x(225.5, "mm"), 15,
CELL_META$cell.xlim[2] + convert_x(279, "mm"), 16,
col ="#E64B35FF", border = NA)
绘制图例
lgd = Legend(title = "expression",col_fun = col_fun1)
draw(lgd,x = unit(0.55,"npc"),y = unit(0.5,"npc"))
circos.clear()
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