dartR.base (version 1.0.5)

gl.report.bases: Reports summary of base pair frequencies

Description

Calculates the frequencies of the four DNA nucleotide bases: adenine (A), cytosine (C), 'guanine (G) and thymine (T), and the frequency of transitions (Ts) and transversions (Tv) in a DArT genlight object.

Usage

gl.report.bases(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL,
  ...
)

Value

The unchanged genlight object

Arguments

x

Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].

plot.display

If TRUE, resultant plots are displayed in the plot window [default TRUE].

plot.theme

Theme for the plot. See Details for options [default theme_dartR()].

plot.colors

List of two color names for the borders and fill of the plots [default c("#2171B5","#6BAED6")].

plot.file

Name for the RDS binary file to save (base name only, exclude extension) [default NULL].

plot.dir

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL, unless specified using gl.set.verbosity].

...

Parameters passed to function ggsave, such as width and height, when the ggplot is to be saved.

Author

Author(s); Arthur Georges. Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr

Details

The function checks first if trimmed sequences are included in the locus metadata (@other$loc.metrics$TrimmedSequence), and if so, tallies up the numbers of A, T, G and C bases. Only the reference state at the SNP locus is counted. Counts of transitions (Ts) and transversions (Tv) assume that there is no directionality, that is C->T is the same as T->C, because the reference state is arbitrary. For presence/absence data (SilicoDArT), it is not possible to count transversions or transitions or transversions/transitions ratio because the SNP data are not available, only a single sequence tag per locus. Only base frequencies are provided. A color vector can be obtained with gl.select.colors() and then passed to the function with the plot.colors parameter. If a plot.file is given, the ggplot arising from this function is saved as an "RDS" binary file using saveRDS(); can be reloaded with readRDS(). A file name must be specified for the plot to be saved. If a plot directory (plot.dir) is specified, the ggplot binary is saved to that directory; otherwise to the tempdir(). To avoid issues from inadvertent use of this function in an assignment statement, the function returns the genlight object unaltered.

See Also

Other matched reports: gl.mahal.assign(), gl.report.factorloadings(), gl.report.fstat(), gl.report.monomorphs()

Examples

# SNP data
  out <- gl.report.bases(testset.gl)
  col <- gl.select.colors(select=c(6,1),palette=rainbow, verbose=0)
  out <- gl.report.bases(testset.gl,plot.colors=col)
# Tag P/A data
  out <- gl.report.bases(testset.gs)