本节来介绍如何通过circlize绘制高级基因组图，后台回复20210719获取本文代码；喜欢的小伙伴欢迎扫描文末二维码加入我的交流群，更多精彩内容为您而准备
加载R包
library(tidyverse)
library(circlize)
library(ComplexHeatmap)
构建数据
set.seed(123)
bed <- generateRandomBed(nr=20,fun = function(k) sample(letters,k,replace = TRUE)) %>%
rename(gene=value1)
bed1 <- generateRandomBed(nr=50,nc =3) %>%
filter(value1 > 0 | value2 > 0.2& value3 < -0.1) %>%
head(20)
绘制染色体轨道
circos.genomicLabels自定义添加标签
circos.initializeWithIdeogram(plotType = NULL)
circos.genomicLabels(bed, labels.column = 4, side = "outside",
col = as.numeric(factor(bed[[1]])),
line_col = as.numeric(factor(bed[[1]])))
circos.genomicIdeogram()
自定义颜色
col_fun1 = colorRamp2(c(-1,0,0.5,1),
c("#3B9AB2","#78B7C5","#EBCC2A","#E1AF00"))
col_fun2 = colorRamp2(c(-1,0,1),
c("#FF0000","#00A08A","#F2AD00"))
col_fun3 = colorRamp2(c(-1,0,0.5,1),
c("#FF0000","#00A08A","#F2AD00","#F21A00"))
circos.genomicHeatmap绘制内圈
此处我们分批绘制三层内圈
circos.genomicHeatmap(bed1 %>% select(1,2,3,4),col = col_fun1,side = "inside", # 热图方向
heatmap_height = 0.2, # 热图轨道高度
connection_height =mm_h(10), #连接线的高度
border = "white")
circos.genomicHeatmap(bed1 %>% select(1,2,3,5),col = col_fun2,
side = "inside",
connection_height=NULL, # NULL不显示连接线
heatmap_height = 0.15,
border = "white")
circos.genomicHeatmap(bed1 %>% select(1,2,3,6),col = col_fun3,
side = "inside",
connection_height=NULL,
heatmap_height = 0.15,
border = "white")
ComplexHeatmap绘制图例
此处通过ComplexHeatmap包提供的Legend函数自定义绘制图例
lgd1 = Legend(col_fun = col_fun1,title="group1",at =c(-1,0,0.5,1))
draw(lgd1,x = unit(0.9,"npc"), y = unit(0.8,"npc"),just = c("right","top"))
lgd2 = Legend(col_fun = col_fun2,title="group2",at =c(-1,0,1))
draw(lgd2,x = unit(0.9,"npc"), y = unit(0.6,"npc"),just = c("right","top"))
lgd3 = Legend(col_fun = col_fun3,title="group3",at =c(-1,0,0.5,1))
draw(lgd3,x = unit(0.9,"npc"), y = unit(0.4,"npc"),just = c("right","top"))
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