## ----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') ## ----out.width='75%', echo=F-------------------------------------------------- knitr::include_graphics("figures/igraph1.jpeg") ## ----out.width='75%', echo=F-------------------------------------------------- knitr::include_graphics("figures/igraph2.jpeg")