Reassortment is an important strategy for influenza A viruses to introduce a HA subtype that is new to human populations, which creates the possibilities of pandemic.

A diagram showed above (Figure 2 of doi:10.1038/srep25549) is widely used to illustrate the reassortment events. While such diagrams are mostly manually draw and edit without software tool to automatically generate. Here, I implemented the hybrid_plot function for producing publication quality figure of reassortment events.

library(tibble)
library(ggplot2)


n <- 8

virus_info <- tibble(
    id = 1:7,
    x = c(rep(1990, 4), rep(2000, 2), 2009),
    y = c(1,2,3,5, 1.5, 3, 4),
    segment_color = list(
        rep('purple', n),
        rep('red', n),
        rep('darkgreen', n),
        rep('lightgreen', n),
        c('darkgreen', 'darkgreen', 'red', 'darkgreen', 'red', 'purple', 'red', 'purple'),
        c('darkgreen', 'darkgreen', 'red', 'darkgreen', 'darkgreen', 'purple', 'red', 'purple'),
        c('darkgreen', 'lightgreen', 'lightgreen', 'darkgreen', 'darkgreen', 'purple', 'red', 'purple'))
)

flow_info <- tibble(from = c(1,2,3,3,4,5,6),
                    to = c(5,5,5,6,7,6,7))
hybrid_plot(virus_info, flow_info)

Continue reading

![](https://guangchuangyu.github.io/blog_images/2016/Screen Shot 2016-11-17 at 8.20.21 PM.png)

这是高老师文章里的图,每一个小图都是通过比较两条比对序列差异而做出来的,从图A和B中可以看出,CF_YL21有可能是Mont和Oz两条序列重组而来。高老师自己做出这图后,深知手工统计序列差异、画图、拼图之困难。问我有没有办法读两条序列,生成一个图。

Continue reading

Author's picture

Guangchuang Yu

Bioinformatics Professor @ SMU

Bioinformatics Professor

Guangzhou