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plot_kaks

Source: R/plot_kaks.R
plot_kaks.Rd

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

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)
#> Joining with `by = join_by(seq1, seq2)`
#> Joining with `by = join_by(seq1, seq2)`
#> Joining with `by = join_by(seq1, seq2)`
g <- plot_kaks(hiv_kaks)