24. 和弦图绘制
清除当前环境中的变量
rm(list=ls())
设置工作目录
setwd("C:/Users/Dell/Desktop/R_Plots/24chord/")
使用circlize包绘制和弦图
# 安装并加载所需的R包
# install.packages("circlize")
library(circlize)
## Warning: package 'circlize' was built under R version 3.6.3
## ========================================
## circlize version 0.4.10
## CRAN page: https://cran.r-project.org/package=circlize
## Github page: https://github.com/jokergoo/circlize
## Documentation: https://jokergoo.github.io/circlize_book/book/
##
## If you use it in published research, please cite:
## Gu, Z. circlize implements and enhances circular visualization
## in R. Bioinformatics 2014.
##
## This message can be suppressed by:
## suppressPackageStartupMessages(library(circlize))
## ========================================
# 构建示例数据
set.seed(999)
# 构造邻接矩阵
mat = matrix(sample(18, 18), 3, 6)
rownames(mat) = paste0("S", 1:3)
colnames(mat) = paste0("E", 1:6)
head(mat)
## E1 E2 E3 E4 E5 E6
## S1 4 14 13 17 5 2
## S2 7 1 6 8 12 15
## S3 9 10 3 16 11 18
# 构建邻接列表数据框
df = data.frame(from = rep(rownames(mat), times = ncol(mat)), #起始对象
to = rep(colnames(mat), each = nrow(mat)), #终止对象
value = as.vector(mat),#起始对象与终止对象之间的相互作用强度
stringsAsFactors = FALSE)
head(df)
## from to value
## 1 S1 E1 4
## 2 S2 E1 7
## 3 S3 E1 9
## 4 S1 E2 14
## 5 S2 E2 1
## 6 S3 E2 10
# 使用chordDiagram函数绘制和弦图
# 使用邻接矩阵绘图
chordDiagram(mat)
# 结束绘图，返回默认设置，否则会继续叠加图层
circos.clear()
image.png
# 使用邻接列表数据框绘图
chordDiagram(df)
circos.clear()
image.png
# 使用order参数调整外围sectors的排列顺序
chordDiagram(mat,
order = c("S2", "S1", "E4", "E1", "S3",
"E5", "E2", "E6", "E3"))
circos.clear()
image.png
# 使用grid.col参数调整外围sectors的填充颜色
grid_col = c(S1 = "red", S2 = "green", S3 = "blue",
E1 = "yellow", E2 = "pink", E3 = "orange",
E4 = "purple", E5 = "black", E6 = "grey")
# transparency参数调整透明度
chordDiagram(mat,
grid.col = grid_col,
transparency = 0.7)
circos.clear()
image.png
# 使用col参数调整links的填充颜色
col_mat = rand_color(length(mat), transparency = 0.5)
head(col_mat)
## [1] "#A4566980" "#91874C80" "#8E9BB680" "#C2D1BC80" "#48484980" "#D1ACBD80"
chordDiagram(mat,
col = col_mat)
circos.clear()
image.png
# 使用link.border，link.lty和link.lwd参数设置links的边框颜色，线型和线宽
chordDiagram(mat,
link.border = "red",
link.lty = 2,
link.lwd = 2)
circos.clear()
image.png
# 使用annotationTrack参数指定外围sectors的类型，可从c("name", "grid", "axis")中指定任意值，也可以指定多个值
chordDiagram(mat, grid.col = grid_col,
annotationTrack = "grid" # 指定类型为“gird”只显示网格，不显示刻度线和标签轨道
)
image.png
chordDiagram(mat, grid.col = grid_col,
annotationTrack = c("name", "grid"), # 指定显示标签和网格轨道
annotationTrackHeight = c(0.04, 0.02) # 指定标签和网格轨道的高度
)
image.png
chordDiagram(mat, grid.col = grid_col,
annotationTrack = NULL) # 去除所有轨道
circos.clear()
image.png
# 使用circos.par函数设置参数
circos.par(clock.wise = FALSE, #逆时针旋转
start.degree = 60 #起始位置设置为逆时针60度方向
)
chordDiagram(mat)
circos.clear()
image.png
#设置不同sector之间gap的间隔大小
circos.par(gap.after = c("S1" = 5, "S2" = 8, "S3" = 15,
"E1" = 5, "E2" = 10,"E3" = 5,
"E4" = 3, "E5" = 5, "E6" = 15))
chordDiagram(mat)
circos.clear()
image.png
sessionInfo()
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18363)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=Chinese (Simplified)_China.936
## [2] LC_CTYPE=Chinese (Simplified)_China.936
## [3] LC_MONETARY=Chinese (Simplified)_China.936
## [4] LC_NUMERIC=C
## [5] LC_TIME=Chinese (Simplified)_China.936
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] circlize_0.4.10
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.5 digest_0.6.20 grid_3.6.0
## [4] magrittr_1.5 evaluate_0.14 stringi_1.4.3
## [7] GlobalOptions_0.1.2 rmarkdown_1.13 tools_3.6.0
## [10] stringr_1.4.0 xfun_0.8 yaml_2.2.0
## [13] compiler_3.6.0 colorspace_1.4-1 shape_1.4.4
## [16] htmltools_0.3.6 knitr_1.23
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