plot_kaks: plot_kaks

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

plot_kaks

Description

This function plots Ka/Ks results obtained via 'rbh2kaks()' function or 'MSA2dist::dnastring2kaks()' function.

Usage

plot_kaks(
  kaks,
  dag = NULL,
  gene.position.cds1 = NULL,
  gene.position.cds2 = NULL,
  tandem.dups.cds1 = NULL,
  tandem.dups.cds2 = NULL,
  PlotTitle = "Ka/Ks results",
  PlotType = "h",
  binw = 0.05,
  splitByChr = FALSE,
  colorBy = "none",
  ka.max = 5,
  ks.max = 5,
  ka.min = 0,
  ks.min = 0,
  select.chr = NULL,
  doPlot = TRUE
)

Arguments

kaks	specify Ka/Ks input obtained via 'rbh2kaks()' [mandatory]
dag	specify DAGchainer results as obtained via 'rbh2dagchainer()' [default: NULL]
gene.position.cds1	specify gene position for cds1 sequences (see cds2genepos) [default: NULL]
gene.position.cds2	specify gene position for cds2 sequences (see cds2genepos) [default: NULL]
tandem.dups.cds1	specify tandem duplicates for cds1 sequences (see tandemdups) [default: NULL]
tandem.dups.cds2	specify tandem duplicates for cds2 sequences (see tandemdups) [default: NULL]
PlotTitle	specify Plot title [default: Ka/Ks results]
PlotType	specify Plot type: "h" histogram or "d" dotplot [default: h]
binw	specify binwidth (see geom_histogram) [default: 0.05]
splitByChr	specify if plot should be split by chromosome [default: FALSE]
colorBy	specify if Ka/Ks gene pairs should be colored by "rbh_class", "dagchainer", "tandemdups" or "none" [default: rbh_class]
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]
doPlot	specify plot [default: TRUE]

Value

Ka/Ks plot

Author(s)

Kristian K Ullrich

Examples

## load example sequence data
data("ath_aly_ncbi_kaks", package="CRBHits")
## plot Ka/Ks values - default
g <- plot_kaks(ath_aly_ncbi_kaks)
## Calculate Ka/Ks values based on MSA
data("hiv", package="MSA2dist")
hiv_kaks <- MSA2dist::dnastring2kaks(hiv)
g <- plot_kaks(hiv_kaks)

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