plot_dagchainer: plot_dagchainer

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

plot_dagchainer

Description

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(s)

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"))

kullrich/CRBHits documentation built on Nov. 13, 2024, 7:44 a.m.