karyoploteR 基因组覆盖图

karyoploteR
karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.

github
https://bernatgel.github.io/karyoploter_tutorial/
（tutorial中提供了各种范图，有点美）

R版本：3.6.1 （避免走弯路，请使用该版本，尝试了3.6.3 和3.5.3，都不能正常导入karyoploteR，缺少各种依赖包）
R中导入安装karyoploteR 包

（1）kpPlotBAMDensity

library(karyoploteR)
kp <- plotKaryotype(genome = "hg38")
data='R0103127.bwa.sort.bam'
kp <- kpPlotBAMDensity(kp, data=data, col='red')

完成后的示意图： 图片.png

（2）kpPlotBAMCoverage

library(karyoploteR)
kp <- plotKaryotype(genome = "hg38", chromosomes = "chr2")
data='R0103127.bwa.sort.bam'
kp <- kpPlotBAMCoverage(kp, data=data, max.valid.region.size = 2e10)

两种绘图优缺点：
kpPlotBAMDensity可以从看全基因组层面看，基本的覆盖情况，成图快；
kpPlotBAMCoverage成图慢，不适合全基因组看，适合选择小区域进行