Add Ideogram Annotation to Coverage Plot.

Add Ideogram Annotation to Coverage Plot.

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,
  highlight.centromere = FALSE,
  highlight.color = "green",
  highlight.alpha = 0.7,
  highlight.line.size = 1,
  highlight.shadow.color = "black",
  highlight.shadow.alpha = 0.7,
  highlight.shadow.line.size = 1,
  plot.space = 0.1,
  plot.height = 0.1
)

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.
highlight.centromere	Logical value, whether to highlight centromere region. Default: FALSE.
highlight.color	The color to mark centromere region on ideogram. Default: "green".
highlight.alpha	The alpha to mark centromere region on ideogram. Default: 0.7.
highlight.line.size	The line size to mark centromere region on ideogram. Default: 1.
highlight.shadow.color	The color to fill centromere shadow polygon. Default: "black".
highlight.shadow.alpha	The alpha of centromere shadow polygon. Default: 0.7.
highlight.shadow.line.size	The line size of centromere 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.

Value

Plot.