ggplot画gene structure和alternative splicing | ggbio | GenomicFeatures

见上篇：genome browser | ggplot | 基因组可视化 | R | transcript | isoform

 

新需求（画出Fig 4D上面的辅图， Science, 2021）：

 

山寨版，分析解构：

• 首先去method里找，完全没写是什么工具画的，那就猜吧；
• 其次看配色和对齐方式，基本肯定是ggplot画的，但仍然查不到是什么工具；
• 最后，能猜到这是卡通图，并不是真实的数据（exon的长度过于平均）；
• 优点：辅图一目了然的AS event可视化，这种barplot的可视化（颜色对应，PSI和为1）更加易读，可以看出作者在AS可视化上的功底；
• 细节也很到位：箭头和UTR

 

做一个API，自动读取AS event格式，添加箭头和UTR，以后可以常用。

 

不难

举个栗子：

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# prepare kartoon data # SE, Cassettes AS_1 <- data.frame(EXONSTART=c(0,2,4),                    EXONEND=c(1,3,5),                    EXONSTRAND="+") seg_1 <- data.frame(x=c(0, 1.5, 3.5),                    xend=c(1.5, 3.5, 4.5),                    y=0, yend=0) AS_2 <- data.frame(EXONSTART=c(0,4),                    EXONEND=c(1,5),                    EXONSTRAND="+") seg_2 <- data.frame(x=c(0, 1.5, 2.5, 3.5),                    xend=c(1.5, 2.5, 3.5, 4.5),                    y=0, yend=0)   options(repr.plot.width=2.5, repr.plot.height=1) p1 <- ggplot() +   # add line and arrow   # geom_hline(yintercept=0)+   # geom_segment(x = 0, xend = 5.5, y = 0, yend = 0) +   geom_segment(data=seg_1, aes(x=x,y=y,xend=xend,yend=yend), arrow=arrow(length=unit(0.3,"cm")), size=1) +   # add exons   geom_rect(data=AS_1, aes(xmin=EXONSTART, xmax=EXONEND,ymin= -0.1,ymax=0.1),fill="#4DAF4A")+   # add UTR   # geom_rect(data=UTR, aes(xmin=EXONSTART, xmax=EXONEND,ymin= -0.05,ymax=0.05),fill="#282a73")+   # details   labs(title = NULL,subtitle = NULL)+   theme_void() +   theme(legend.position = "none") +   scale_x_continuous(expand = c(0.1, 0.1), limits = c(0, 5)) +   scale_y_continuous(expand = c(0.02, 0.02), limits = c(-0.1, 0.1)) p1   options(repr.plot.width=2.5, repr.plot.height=1) p2 <- ggplot() +   # add line and arrow   # geom_hline(yintercept=0)+   # geom_segment(x = 0, xend = 5.5, y = 0, yend = 0) +   geom_segment(data=seg_2, aes(x=x,y=y,xend=xend,yend=yend), arrow=arrow(length=unit(0.3,"cm")), size=1) +   # add exons   geom_rect(data=AS_2, aes(xmin=EXONSTART, xmax=EXONEND,ymin= -0.1,ymax=0.1),fill="#984EA3")+   # add UTR   # geom_rect(data=UTR, aes(xmin=EXONSTART, xmax=EXONEND,ymin= -0.05,ymax=0.05),fill="#282a73")+   # details   labs(title = NULL,subtitle = NULL)+   theme_void() +   theme(legend.position = "none") +   scale_x_continuous(expand = c(0.1, 0.1), limits = c(0, 5))+   scale_y_continuous(expand = c(0.02, 0.02), limits = c(-0.1, 0.1)) p2   options(repr.plot.width=2.5, repr.plot.height=2) AS1 <- cowplot::plot_grid(p1,p2,ncol = 1) AS1   options(repr.plot.width=9, repr.plot.height=1) cowplot::plot_grid(AS2, AS2, AS3, AS1,ncol = 4)

　　

最终的模仿图，颜值还行：

 

 

分析案例：project/scPipeline/AS/suppa_AS_stat.ipynb

 

参考：

• "ggplot2 exercise" drawing gene structure diagram
• ggbio: visualization toolkits for genomic data
• ggscaleRanges
• Introduction to ‘gggenes’
• Example Needed: Using arrow() with ggplot2
• ggplot2 画个基因结构示意图