Add Genome Links to Coverage Plot.
Usage
# 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
- score.col
Column index that contains score information, used when
file.typeis bedpe. Default: NULL.- score.threshold
The score threshold, used when
score.colis not NULL. Default: NULL.- score.color
The score color vector. Default: c("grey70", "#56B1F7", "#132B43").
- scale.range
Scale the height of links according to width, should be greater than or equal to 1 (not scale). Default: 10.
- plot.space
Top and bottom margin. Default: 0.1.
- plot.height
The relative height of link to coverage plot. Default: 0.2.
- arrow.size
The size of the arrow head. Default: 0.02.
- remove_x_axis
Logical value, whether to remove the x-axis. Default: FALSE.
- link_plot_on_top
Logical value, whether to plot the link plot on top of the coverage plot. Default: FALSE.
- extend.base
Extend the base pair range to show more information. Default: 1000000.
- show.rect
Logical value, whether to add rect border to the plot. Default: FALSE.
- x.range
The range of x-axis to show. Default: NULL.
- log.scale
Logical value, whether to log1p the score. Default: TRUE.
- link.file
File contains region link information.
- file.type
The type of
link.file, choose from bedpe, pairs. Default: bedpe.- plot.curve
One of 'curve' or 'bezier', for the latter it is required to install package
ggforce. Default: 'curve'.