inst/doc/reassortment.R

In seqcombo: Visualization Tool for Sequence Recombination and Reassortment

## ----style, echo=FALSE, results="asis", message=FALSE-------------------------
knitr::opts_chunk$set(tidy = FALSE,
		   message = FALSE)

## ----echo=FALSE, results="hide", message=FALSE--------------------------------
library("seqcombo")
library(tibble)
library(emojifont)
library(ggplot2)

## ----fig.width=8, fig.height=7------------------------------------------------
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)

## ----fig.width=8, fig.height=7------------------------------------------------
hybrid_plot(virus_info, flow_info, v_color='firebrick', v_fill='darkgreen', l_color='steelblue')

## ----fig.width=8, fig.height=7------------------------------------------------
virus_info$Host = c("Avian", "Human", rep("Swine", 4), "Human")
hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host)

## ----fig.width=8, fig.height=7------------------------------------------------
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)

## ----fig.width=9, fig.height=8------------------------------------------------
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)

## ----fig.width=10, fig.height=9, out.width="80%"------------------------------
hybrid_plot(virus_info, flow_info, v_color=~Host, v_fill=~Host, asp=2)

## ----fig.width=7.5, fig.height=7----------------------------------------------
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)
          )

## ----fig.width=9, fig.height=7------------------------------------------------
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))

## ----fig.width=8, fig.height=7, fig.showtext=TRUE-----------------------------
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()

## ----fig.height=7, fig.showtext=TRUE------------------------------------------
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')

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knitr::include_graphics("figures/igraph1.jpeg")

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knitr::include_graphics("figures/igraph2.jpeg")