Make Oxford Plots

Takes a GBreaks object and prepares an Oxford (macrosynteny) of the coordinates of the query ranges against the target ranges after concatenating them.

Usage

makeOxfordPlots(
  gb,
  sp1Name = "target",
  sp2Name = "query",
  sp1ChrArms = NULL,
  sp2ChrArms = NULL,
  type = c("line", "point", "none"),
  size = 1,
  diag = TRUE,
  col = c("seqnames", "strand", "score")
)

Arguments

gb

A GBreaks object

sp1Name

Name of the first species (default: sp1)

sp2Name

Name of the second species (default: sp2)

sp1ChrArms

A GBreaks object of chromosome arms in sp1 genome

sp2ChrArms

A GBreaks object of chromosome arms in sp2 genome

type

The type of the plot (point, line or none)

size

The size of the plotted dots or segments.

diag

Diagonalise the plot by reordering query sequence levels.

col

Colour of the plotted dots or lines by seqnames, strand or score.

Value

Returns a ggplot2 object that can be further modified using the + operator. Use type = 'none' to receive an object without geom layer.

See also

Other plot functions: bp_heatmap(), bp_pair_analysis(), feature_coverage(), plotApairOfChrs()

Author

Aleksandra Bliznina

Charles Plessy

Examples

makeOxfordPlots(exampleTranslocation)

makeOxfordPlots(exampleTranslocation, type = "p")