plot genomic ranges and links

plot genomic ranges and links

Usage

# S4 method for class 'linkSet'
plot_genomic_ranges(
  linkset,
  showBait = NULL,
  showOE = NULL,
  x.range = NULL,
  score.col = "count",
  show.rect = TRUE,
  extend.base = 1e+06,
  ...,
  bait_col = "red",
  oe_col = "DeepSkyBlue3",
  default_col = "grey",
  vjust = NULL,
  linejoin = "mitre",
  na.rm = FALSE,
  minimal_width = 0.01,
  show.legend = NA,
  inherit.aes = TRUE,
  link_plot_on_top = FALSE,
  arrow.size = 0.05,
  remove_x_axis = FALSE,
  plot.height = 0.4,
  plot.space = 0.1,
  log.scale = TRUE
)

Arguments

linkset

A linkSet object.

showBait

A character vector specifying the bait region to be shown. Default: NULL.

showOE

A GRanges object specifying the oe region to be shown. Default: NULL.

x.range

A numeric vector of length 2 specifying the x-axis range. Default: NULL.

score.col

A character string specifying the column name of the score. Default: "count".

show.rect

Logical value, whether to show the rectangle. Default: TRUE.

extend.base

A numeric value specifying the extension base. Default: 1000000.

...

Additional arguments.

bait_col

A character string specifying the color of the bait region. Default: "red".

oe_col

A character string specifying the color of the oe region. Default: "DeepSkyBlue3".

default_col

A character string specifying the color of the default region. Default: "grey".

vjust

A numeric value specifying the vertical justification. Default: NULL.

linejoin

A character string specifying the line join. Default: "mitre".

na.rm

Logical value, whether to remove NA values. Default: FALSE.

minimal_width

A numeric value specifying the minimal width. Default: 0.01.

show.legend

Logical value, whether to show the legend. Default: NA.

inherit.aes

Logical value, whether to inherit the aesthetics. Default: TRUE.

link_plot_on_top

Logical value, whether to plot the link plot on top of the coverage plot. Default: FALSE.

arrow.size

A numeric value specifying the size of the arrow head. Default: 0.05.

remove_x_axis

Logical value, whether to remove the x-axis. Default: FALSE.

plot.height

A numeric value specifying the height of the plot. Default: 0.4.

plot.space

A numeric value specifying the space between the plot and the link plot. Default: 0.1.

log.scale

Logical value, whether to log scale the score. Default: TRUE.

Value

A ggplot object.

Examples

data(linkExample)
plot_genomic_ranges(linkExample, extend.base = 10)
#> Warning: score.col not found, using count as default