在 circlize 中添加基因组特征轨迹时出错

Question

我正在尝试使用 BED 文件中的简单基因组符号生成 circos 图。但是，当我使用 circos.genomeRect 时，这会导致错误，或者在不绘制矩形但绘制半圆的轨道中，如下所示。

考虑以下可重现的示例：

library("circlize")
library("tidyverse")

circos.par(start.degree = 90,
           cell.padding = c(0, 0, 0, 0),
           #points.overflow.warning=FALSE,
           track.height = 0.10   
)

# Initialize genome (bed file with genome sizes)
genome <- tibble(chr=c("chr1","chr2"), start = c(1,1), end = c(6000000, 3000000))
circos.genomicInitialize(genome, plotType = c("axis"), major.by = 1000000)

# Add track with annotation
feature <- tibble(chr = c("chr1", "chr1"), start = c(2500, 4500000), end = c(4150000, 6350000))
circos.genomicTrack(feature, ylim=c(0,1),
                    panel.fun = function(region, value, ...) {
                      circos.genomicRect(region, value, ytop.column = 1, ybottom = 0, col="blue")
                    })
circos.clear()

这returns一个错误：

Error in if (sum(l) && circos.par("points.overflow.warning")) { : missing value where TRUE/FALSE needed

In addition: Warning message: In is.na(x) | is.na(y) : Error in if (sum(l) && circos.par("points.overflow.warning")) { : missing value where TRUE/FALSE needed

此时，如果在上面的circos.par中设置了points.overflow.warning=FALSE，则错误消失，但一定是出现了其他错误，即不绘制矩形：

我错过了什么吗？这个简单的例子有什么问题？谢谢

编辑

我刚刚注意到我绘制的特征数据框有一个坐标错误，因为它比染色体的实际大小延伸得更长。但是，如果这是固定的，例如：feature <- tibble(chr = c("chr1", "chr1"), start = c(2500, 4500000), end = c(4150000, 5350000))，则会出现新的错误！！

Warning message: In is.na(x) | is.na(y) : longer object length is not a multiple of shorter object length

Answer 1

它似乎适用于 data.frames 而不是 tibbles:

library("circlize")

circos.par(start.degree = 90,
           cell.padding = c(0, 0, 0, 0),
           #points.overflow.warning=FALSE,
           track.height = 0.10   
)

# Initialize genome (bed file with genome sizes)
genome <- data.frame(chr=c("chr1","chr2"), start = c(1,1), end = c(6000000, 3000000))
circos.genomicInitialize(genome, plotType = c("axis"), major.by = 1000000)

# Add track with annotation
feature <- data.frame(chr = c("chr1", "chr1"), start = c(2500, 4500000), end = c(4150000, 5350000))


circos.genomicTrack(feature, ylim=c(0,1),
                    panel.fun = function(region, value, ...) {
                      circos.genomicRect(region, value, col="blue")
                    })

circos.clear()

^{由 reprex package (v0.3.0)}

于 2020-08-11 创建

在 circlize 中添加基因组特征轨迹时出错

Errors adding genomic feature track in circlize

r

plot

circlize

circos