checkSpecLocus: Barplot of Species Numbers per Locus

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Produce a barplot showing the number of species found for each locus. Thereby the number of species either refers to the number of species found on GenBank, the number of species selected according to identity and coverage, or the number of species included in the final alignment. Additionally, black lines to right of the bars indicate the cumulative species numbers for each locus if this locus was to be concatenated with all other loci having more species.

Usage

checkSpecLocus(
  megProj,
  stage = "selected",
  subset.taxon,
  subset.locus,
  plot = TRUE
)

Arguments

megProj	An object of class megapteraProj.
stage	A vector of mode character; valid are "retrieved", "sel", or "blocks" referring to the number of species (1) found on in the database, (2) selected according to coverage and identity (see locus); or included in the final alignment, respectively.
subset.taxon	A vector of mode "character", that can be used to choose a subset of the total taxa available.
subset.locus	A vector of mode "character", that can be used to choose a subset of the total loci available.
plot	Logical, indicating if the barplot should be produced on the current graphical device or not.

Value

A list, but mainly called for its side effect, the plotting of a barplot.

See Also

checkMissingSpec to create a table of species that were missed/lost during consecutive steps of the pipeline.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.