Creates a visualization of genomic links for a linkSet object
Usage
geom_linkset(
linkSet,
score.col = "count",
score.threshold = NULL,
score.color = c("grey70", "#56B1F7", "#132B43"),
scale.range = 10,
plot.space = 0.1,
plot.height = 0.2,
arrow.size = 0.05,
remove_x_axis = FALSE,
link_plot_on_top = FALSE,
extend.base = 10000,
show.rect = FALSE,
x.range = NULL,
log.scale = TRUE
)
# S4 method for class 'linkSet'
geom_linkset(
linkSet,
score.col = "count",
score.threshold = NULL,
score.color = c("grey70", "#56B1F7", "#132B43"),
scale.range = 10,
plot.space = 0.1,
plot.height = 0.2,
arrow.size = 0.05,
remove_x_axis = FALSE,
link_plot_on_top = FALSE,
extend.base = 1e+06,
show.rect = FALSE,
x.range = NULL,
log.scale = TRUE
)Arguments
- linkSet
A linkSet object
- score.col
Column name containing score information (default: "count")
- score.threshold
Score threshold for filtering links (default: NULL)
- score.color
Color vector for score visualization (default: c("grey70", "#56B1F7", "#132B43"))
- scale.range
Scale factor for link height (default: 10)
- plot.space
Top and bottom margin (default: 0.1)
- plot.height
Relative height of link to coverage plot (default: 0.2)
- arrow.size
Size of arrow heads (default: 0.05)
- remove_x_axis
Whether to remove x-axis (default: FALSE)
- link_plot_on_top
Whether to plot links above coverage (default: FALSE)
- extend.base
Base pair extension range (default: 10000)
- show.rect
Whether to show rectangle borders (default: FALSE)
- x.range
Range for x-axis (default: NULL)
- log.scale
Whether to use log scale for scores (default: TRUE)