geom_hybrid: geom_hybrid

Description Usage Arguments Value Author(s) Examples

View source: R/reassortment.R

Description

geom layer for reassortment events

Usage

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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")

Arguments

virus_info

virus information

flow_info

flow 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

parse

whether parse label, only works if 'label' and 'label_position' exist

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)

t_size

size of text label

t_color

color of text label

Value

geom layer

Author(s)

Guangchuang Yu

Examples

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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))

ggplot() + geom_hybrid(virus_info, flow_info)

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