Plots a pair of chromosomes from a GBreaks object.

Plots the mapping between a pair of chromosomes using the genoPlotR::plot_gene_map function. One sequence feature (usually a chromosome) is selected from the target genome. The corresponding sequence feature on the query genome is either chosen automatically (being the one with the largest fraction of the mappings) or given as a parameter.

Usage

plotApairOfChrs(
  gb,
  chrT = NULL,
  chrQ = NULL,
  dna_seg_scale = TRUE,
  dna_seg_labels = NULL,
  ...
)

Arguments

gb

A GBreaks object.

chrT

A sequence name on the target genome. Defaults to the first sequence level of the gb object.

chrQ

(Optional) A sequence name on the query genome. Defaults to the longest cumulative match on chrT.

dna_seg_scale

Plot coordinats and a scale bar (defaults to TRUE).

dna_seg_labels

A character vector to override default labels for sequence names.

...

Further arguments are passed to plot_gene_map.

Value

Plots to the active device and returns and oma::oma_layout object like the genoPlotR::plot_gene_map function.

Note

In this kind of plot, the ranges from the selected sequence on the target genome that are not mapped to the query sequence are not displayed.

See also

Other genoPlotR functions: gb2comp(), gb2dna_seg(), gb2xlim(), gr2dna_seg()

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

Other Structural variants: StructuralVariants, flagDoubleInversions(), flagInversions(), flagPairs(), flagTranslocations()

Author

Charles Plessy

Examples

plotApairOfChrs(exampleInversion)

plotApairOfChrs(exampleDeletion)


# Labels can be overriden.
plotApairOfChrs(exampleDeletion, dna_seg_labels = c("over...", "...ridden"))