Package seqcombo. R topics documented: March 10, 2019

Transcription

1 Package seqcombo March 10, 2019 Title Visualization Tool for Sequence Recombination and Reassortment Version Provides useful functions for visualizing sequence recombination and virus reassortment events. Depends R (>= 3.4.0) Imports Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, rvcheck, utils Suggests emojifont, knitr, prettydoc, tibble VignetteBuilder knitr ByteCompile true License Artistic-2.0 Encoding UTF-8 LazyData true BugReports biocviews Alignment, Software, Visualization RoxygenNote git_url git_branch master git_last_commit aaca2d3 git_last_commit_date Date/Publication Author Guangchuang Yu [aut, cre] Maintainer Guangchuang Yu <guangchuangyu@gmail.com> R topics documented: geom_genotype geom_hybrid hybrid_plot plot seqdiff set_layout show simplot

2 2 geom_genotype Index 9 geom_genotype geom_genotype geom layer of genotype geom_genotype(virus_info, v_color = "darkgreen", v_fill = "steelblue", v_shape = "ellipse", l_color = "black", asp = 1, g_height = 0.65, g_width = 0.65) virus_info v_color v_fill v_shape l_color asp g_height g_width virus information the color of outer boundary of virus; can use expression (e.g. v_color=~host) to color virus by specific variable the color to fill viruses; can use expression (e.g. v_fill=~host) to fill virus by specific variable one of hexagon or ellipse color of the lines that indicate genetic flow aspect ratio of the plotting device height of regions to plot gene segments relative to the virus width of gene segment relative to width of the virus (the hexagon) geom layer 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'))) ggplot() + geom_genotype(virus_info)

3 geom_hybrid 3 geom_hybrid geom_hybrid geom layer for reassortment events geom_hybrid(virus_info, flow_info, v_color = "darkgreen", v_fill = "steelblue", v_shape = "ellipse", l_color = "black", asp = 1, parse = FALSE, g_height = 0.65, g_width = 0.65, t_size = 3.88, t_color = "black") virus_info flow_info v_color v_fill v_shape l_color asp parse g_height g_width t_size t_color virus information flow information the color of outer boundary of virus; can use expression (e.g. v_color=~host) to color virus by specific variable the color to fill viruses; can use expression (e.g. v_fill=~host) to fill virus by specific variable one of hexagon or ellipse color of the lines that indicate genetic flow aspect ratio of the plotting device whether parse label, only works if label and label_position exist height of regions to plot gene segments relative to the virus width of gene segment relative to width of the virus (the hexagon) size of text label color of text label geom layer Guangchuang Yu 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),

4 4 hybrid_plot 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)) ggplot() + geom_hybrid(virus_info, flow_info) hybrid_plot hyrid_plot visualize virus reassortment events hybrid_plot(virus_info, flow_info, v_color = "darkgreen", v_fill = "steelblue", v_shape = "ellipse", l_color = "black", asp = 1, parse = FALSE, g_height = 0.65, g_width = 0.65, t_size = 3.88, t_color = "black") virus_info flow_info v_color v_fill v_shape l_color asp parse g_height g_width t_size t_color virus information flow information the color of outer boundary of virus; can use expression (e.g. v_color=~host) to color virus by specific variable the color to fill viruses; can use expression (e.g. v_fill=~host) to fill virus by specific variable one of hexagon or ellipse color of the lines that indicate genetic flow aspect ratio of the plotting device whether parse label, only works if label and label_position exist height of regions to plot gene segments relative to the virus width of gene segment relative to width of the virus (the hexagon) size of text label color of text label ggplot object

5 plot 5 library(tibble) 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) plot plot method for SeqDiff object plot method for SeqDiff object ## S4 method for signature 'SeqDiff,ANY' plot(x, width = 50, title = "auto", xlab = "Nucleotide Position", by = "bar", fill = "firebrick", colors = c(a = "#E495A5", C = "#ABB065", G = "#39BEB1", T = "#ACA4E2"), xlim = NULL) x width title xlab by fill colors xlim SeqDiff object bin width plot title xlab one of bar and area fill color of upper part of the plot color of lower part of the plot limits of x-axis plot

6 6 set_layout fas <- list.files(system.file("examples","gvariation", package="seqcombo"), pattern="fas", full.names=true) x1 <- seqdiff(fas[1], reference=1) plot(x1) seqdiff seqdiff calculate difference of two aligned sequences seqdiff(fasta, reference = 1) fasta fasta file reference which sequence serve as reference, 1 or 2 SeqDiff object fas <- list.files(system.file("examples","gvariation", package="seqcombo"), pattern="fas", full.names=true) seqdiff(fas[1], reference=1) set_layout set_layout set layout for reassortment plot set_layout(virus_info, flow_info, layout = "layout.auto") virus_info flow_info layout virus information flow information layout method

7 show 7 updated virus_info show show method show method show(object) object SeqDiff object message fas <- list.files(system.file("examples","gvariation", package="seqcombo"), pattern="fas", full.names=true) x1 <- seqdiff(fas[1], reference=1) x1 simplot simplot Sequence similarity plot simplot(file, query, window = 200, step = 20, group = FALSE, id, sep, sd = FALSE)

8 8 simplot file query window step group id sep sd alignment fast file query sequence sliding window size (bp) step size to slide the window (bp) whether grouping sequence position to extract id for grouping; only works if group = TRUE separator to split sequence name; only works if group = TRUE whether display standard deviation of similarity among each group; only works if group=true ggplot object fas <- system.file("examples/gvariation/sample_alignment.fa", package="seqcombo") simplot(fas, 'CF_YL21')

9 Index geom_genotype, 2 geom_hybrid, 3 hybrid_plot, 4 plot, 5 plot,seqdiff,any-method (plot), 5 seqdiff, 6 SeqDiff-class (show), 7 set_layout, 6 show, 7 show,seqdiff-method (show), 7 simplot, 7 9