0.准备输入数据
可以是矩阵
library(circlize)
set.seed(999)
mat = sample(0:5,21,replace = T)
mat = matrix(mat,nrow = 3)
rownames(mat) = paste0("S",1:nrow(mat))
colnames(mat) = paste0("G",1:ncol(mat))
mat
## G1 G2 G3 G4 G5 G6 G7
## S1 2 0 1 2 5 1 2
## S2 3 5 1 4 2 0 1
## S3 4 0 5 5 2 4 3
行是一边，列是一边，矩阵正文的数字表示连接的强度。
可以是tidy数据框
library(tidyr)
library(tibble)
df <- gather(rownames_to_column(as.data.frame(mat),var = "from"),
key = "to",
value = "value",
- from)
head(df)
## from to value
## 1 S1 G1 2
## 2 S2 G1 3
## 3 S3 G1 4
## 4 S1 G2 0
## 5 S2 G2 5
## 6 S3 G2 0
一行是一个连接关系，第一列和第二列是要连接的两边，第三列是连接的强度。
2.简单画图
chordDiagram(mat)
circos.clear()
chordDiagram(df)
circos.clear()
circos.clear()是清除原来的弦图设置。你会发现颜色不一样，这是因为每次画图，颜色是随机的
3.自定义边的颜色
这些颜色出自RColorBrewer包，是我喜欢的配色，可以自己修改
library(RColorBrewer)
col = c(brewer.pal(n = 12,name = "Set3"),
brewer.pal(n = 8,name = "Set2"))
col
## [1] "#8DD3C7" "#FFFFB3" "#BEBADA" "#FB8072" "#80B1D3" "#FDB462" "#B3DE69"
## [8] "#FCCDE5" "#D9D9D9" "#BC80BD" "#CCEBC5" "#FFED6F" "#66C2A5" "#FC8D62"
## [15] "#8DA0CB" "#E78AC3" "#A6D854" "#FFD92F" "#E5C494" "#B3B3B3"
border_color <- sample(col,nrow(mat)+ncol(mat))
chordDiagram(mat, grid.col = border_color, transparency = 0.7)
chordDiagram(t(mat), grid.col = border_color)
从这两张图可以看到，弦默认与行的颜色一致。
4.自定义弦的颜色
还是从刚才的颜色里面取
linkcolor <- sample(col,length(mat),replace = T)
dim(linkcolor) <- dim(mat)
chordDiagram(mat, grid.col = border_color, col = linkcolor,transparency = 0.7)
circos.clear()
linkcolor2 <- colorRamp2(range(mat), c("#FA0A0A", "#FFFFFF"),
transparency = 0.5) # 产生连续色块并指定透明度
chordDiagram(mat, grid.col = border_color, col = linkcolor2)
circos.clear()
