Package 'seqcombo'

geom_genotype

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)

---

geom_hybrid

Description

geom layer for reassortment events

Usage

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

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)

---

hyrid_plot

Description

visualize virus reassortment events

Usage

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"
)

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

ggplot object

Author(s)

Guangchuang Yu

Examples

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)

---

set_layout

Description

set layout for reassortment plot

Usage

set_layout(virus_info, flow_info, layout = "layout.auto")

Arguments

virus_info	virus information
flow_info	flow information
layout	layout method

Value

updated virus_info

Author(s)

Guangchuang Yu

---