gl.report.bases {dartR.base}

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,
  ...
)

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.

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. A color vector can be obtained with gl.select.colors() and then passed to the function with the plot.colors parameter. Themes can be obtained from in

• https://ggplot2.tidyverse.org/reference/ggtheme.html and

• https://yutannihilation.github.io/allYourFigureAreBelongToUs/ggthemes/

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().

Value

The unchanged genlight object

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

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)
  out <- gl.report.bases(testset.gl,plot.colors=col)
# Tag P/A data
  out <- gl.report.bases(testset.gs)