# seqcombo for visualizing genetic reassortment

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)

    ## Warning: `aes_()` was deprecated in ggplot2 3.0.0.
    ## ℹ Please use tidy evaluation idioms with `aes()`
    ## ℹ The deprecated feature was likely used in the seqcombo package.
    ##   Please report the issue at
    ##   <https://github.com/GuangchuangYu/seqcombo/issues>.
    ## This warning is displayed once every 8 hours.
    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    ## generated.

    ## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
    ## ℹ Please use `linewidth` instead.
    ## ℹ The deprecated feature was likely used in the seqcombo package.
    ##   Please report the issue at
    ##   <https://github.com/GuangchuangYu/seqcombo/issues>.
    ## This warning is displayed once every 8 hours.
    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    ## generated.

The `hybrid_plot` requires two tibble data frame of virus information and genetic flow information.

Users need to provide `x` and `y` positions to plot the virus, this make sense for geographically and temporally information are usually available in such phylodynamic study and can be employed to set `x` or `y` to provide more information and help interpretation of the reassortment events.

We use hexagon to represent virus. Users can set the virus outer boundary color by `v_color` and fill the virus by `v_fill`. Color of line segments that indicate the genetic flow relationship can be specify via `l_color` parameter.

    hybrid_plot(virus_info, flow_info, v_color='firebrick', v_fill='darkgreen', l_color='steelblue')

We usually have more information to present, for example host information and HA subtype etc. and these information can be used to color the virus either by `v_color` or `v_fill`

    virus_info$Host = c("Avian", "Human", rep("Swine", 4), "Human")
    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host)

The relative virus size can also be specify if a `virus_size` column is available in the input `virus_info` data.

    virus_info$virus_size <- c(rep(1, 3), 2, 1, 1, 1.5)
    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host)

If `label` and `label_position` coloumns are available, the virus labels (virus name or other information) will be added automatically.

    virus_info$label <- c("Avian", "Human\nH3N2", "Classic\nswine\nH1N1", "Eurasian swine",
                          "North American swine\n triple reassrotant H3N2",
                          "North American swine\n triple reassortant H1N2", "2009 Human H1N1")
    virus_info$label_position <- c('left', 'left', 'left', 'below', 'below', 'upper', 'below')
    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host)

User can use `asp` to set the aspect ratio of hexagons, `asp < 1` for thick/short and `asp > 1` for thin/tall.

    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host, asp=2)

The output of `hybrid_plot` is a `ggplot` object and users can use `ggplot2` to modify the details.

    title <- "Reassortment events in evolution of the 2009 influenza A (H1N1) virus"
    caption <- 'Gene segments: PB2, PB1, PA, HA, NP, NA, M, NS'
    color <- c(Avian="purple", Human="red", Swine="darkgreen")

    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host) +
        labs(caption=caption, title=title) +
        scale_color_manual(values=color) + scale_fill_manual(values=color) +
        scale_x_continuous(breaks=c(1990, 2000, 2009)) +
        xlab(NULL) + ylab(NULL) + theme_minimal() +
        theme(axis.line.y = element_blank(),
              axis.text.y = element_blank(),
              axis.ticks.y = element_blank(),
              panel.grid.minor=element_blank(),
              panel.grid.major.y=element_blank(),
              legend.position = c(.95, .1)
              )

Top-down or bottom-up style is also supported.

    x <- virus_info$x
    virus_info$x <- virus_info$y
    virus_info$y <- x
    virus_info$label_position <- c(rep("right", 3), "left", "left", "right", "right")
    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host) +
        scale_y_reverse() + scale_x_continuous(limits=c(0, 5.5))

User can also use Emoji to label the virus (host information in this example):

    virus_info$label <- c("chicken", "woman", "pig", "pig", "pig", "pig", "woman")
    hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host,
                  parse='emoji', t_size=8, t_color='firebrick') +
        scale_y_reverse()

In case you don’t have xy-coordination information, you can use `set_layout` function to auto setting the xy position using selected layout function.

    virus_info <- set_layout(virus_info, flow_info, layout="layout.kamada.kawai")
    hybrid_plot(virus_info, flow_info, parse='emoji', t_size=8, t_color='firebrick')

    virus_info <- set_layout(virus_info, flow_info, layout="layout.fruchterman.reingold")
    hybrid_plot(virus_info, flow_info, parse='emoji', t_size=8, t_color='firebrick')