circlize

circlize 提供了圈形布局的通用可视化方法。

基本信息

软件包	链接
编程语言	R
CRAN	https://CRAN.R-project.org/package=circlize
GitHub	https://github.com/jokergoo/circlize
文档	https://jokergoo.github.io/circlize_book/book/
论文	Zuguang Gu, et al., circlize Implements and enhances circular visualization in R. Bioinformatics 2014.

例子

绘制简单的 xy 坐标图：

library(circlize)
factors = letters[1:7]
circos.initialize(factors, xlim = c(0, 1))
circos.trackPlotRegion(ylim = c(0, 1), track.height = 0.4, panel.fun = function(x, y) {    
    circos.points(runif(100), runif(100), cex = 0.5)
})

circos.clear()

绘制基因组图：

load(paste(system.file(package = "circlize"), "/extdata/DMR.RData", sep = ""))

circos.initializeWithIdeogram(plotType = c("axis", "labels"))

bed_list = list(DMR_hyper, DMR_hypo)
circos.genomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))

circos.genomicDensity(bed_list[[1]], col = c("#FF000080"), track.height = 0.1)
circos.genomicDensity(bed_list[[2]], col = c("#0000FF80"), track.height = 0.1)

circos.clear()

绘制和弦图（Chord diagram）：

mat = matrix(sample(1:100, 18, replace = TRUE), 3, 6)
rownames(mat) = letters[1:3]
colnames(mat) = LETTERS[1:6]
rn = rownames(mat)
cn = colnames(mat)

chordDiagram(mat)

circos.clear()

更多的例子：