plot_dagchainer

This function plots DAGchainer (http://dagchainer.sourceforge.net/) results obtained via `rbh2dagchainer()` function.

Usage

plot_dagchainer(
  dag,
  DotPlotTitle = "DAGchainer results",
  colorBy = "none",
  kaks = NULL,
  ka.max = 5,
  ks.max = 5,
  ka.min = 0,
  ks.min = 0,
  select.chr = NULL
)

Arguments

dag

specify DAGchainer results as obtained via `rbh2dagchainer()` [mandatory]

DotPlotTitle

specify DotPlot title [default: DAGchainer results]

colorBy

specify if dagchainer groups should be colored by "Ka", "Ks", "Ka/Ks" or "none" [default: none]

kaks

specify Ka/Ks input obtained via `rbh2kaks()` [default: NULL]

ka.max

specify max Ka to be filtered [default: 5]

ks.max

specify max Ks to be filtered [default: 5]

ka.min

specify min Ka to be filtered [default: 0]

ks.min

specify min Ks to be filtered [default: 0]

select.chr

filter results for chromosome names [default: NULL]

Value

synteny plot

Author

Kristian K Ullrich

Examples

## load example sequence data
data("ath_aly_ncbi_dagchainer", package="CRBHits")
## plot DAGchainer results - default
plot_dagchainer(
    dag=ath_aly_ncbi_dagchainer)

## chromosome subset
plot_dagchainer(
    dag=ath_aly_ncbi_dagchainer,
    select.chr=c("NC_000932.1", "NC_034379.1"))