ggcoverage (version 0.7.1)

geom_ideogram: Add Ideogram Annotation to Coverage Plot.

Description

Add Ideogram Annotation to Coverage Plot.

Usage

geom_ideogram(
  genome = "hg19",
  mark.color = "red",
  mark.alpha = 0.7,
  mark.line.size = 1,
  add.shadow = TRUE,
  shadow.color = "grey",
  shadow.alpha = 0.7,
  shadow.line.size = 1,
  plot.space = 0.1,
  plot.height = 0.1
)

Value

Plot.

Arguments

genome

Single specie names, which must be one of the result from ucscGenomes()$db. If missing, will invoke a menu for users to choose from. Default: hg19.

mark.color

The color to mark plot region on ideogram. Default: "red".

mark.alpha

The alpha to mark plot region on ideogram. Default: 0.7.

mark.line.size

The line size to mark plot region on ideogram. Default: 1.

add.shadow

Logical value, whether to add shadow polygon. Default: TRUE.

shadow.color

The color to fill shadow polygon. Default: grey.

shadow.alpha

The alpha of shadow polygon. Default: 0.7.

shadow.line.size

The line size of shadow polygon. Default: 1.

plot.space

Top and bottom margin. Default: 0.1.

plot.height

The relative height of ideogram annotation to coverage plot. Default: 0.2.