geom_genotype: geom_genotype

In seqcombo: Visualization Tool for Sequence Recombination and Reassortment

Description

geom layer of genotype

Usage

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)

Arguments

virus_info	virus information
v_color	the color of outer boundary of virus; can use expression (e.g. v_color=~Host) to color virus by specific variable
v_fill	the color to fill viruses; can use expression (e.g. v_fill=~Host) to fill virus by specific variable
v_shape	one of 'hexagon' or 'ellipse'
l_color	color of the lines that indicate genetic flow
asp	aspect ratio of the plotting device
g_height	height of regions to plot gene segments relative to the virus
g_width	width of gene segment relative to width of the virus (the hexagon)

Value

geom layer

Author(s)

guangchuang yu

Examples

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)

Example output

seqcombo documentation built on Nov. 8, 2020, 6:27 p.m.