gl.report.factorloadings: Reports factor loadings for a PCA or PCoA

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Reports factor loadings for a PCA or PCoA

Description

Extracts the factor loadings from a glPCA object (generated by gl.pcoa) and plots their distribuion.

Usage

gl.report.factorloadings(
  pca,
  axis = 1,
  n.display = 15,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  bins = 25,
  verbose = NULL,
  ...
)

Arguments

pca	Name of the glPCA object containing factor loadings [required].
axis	Axis in the ordination used to display the factor loadings [default 1]
n.display	Number of loci for which to display factorloadings [default 15]
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()]
bins	Number of bins to display in histograms [default 25].
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 extracts the factor loadings for a given axis from a PCA object generated by gl.pcoa and plots their magnitudes. Useful for identifying loci that load high for a given axis.

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.bases(), gl.report.fstat(), gl.report.monomorphs()

Examples

pca <- gl.pcoa(testset.gl)
gl.report.factorloadings(pca = pca)

dartR.base documentation built on April 4, 2025, 2:45 a.m.