gl.plot.structure: Plots STRUCTURE analysis results (Q-matrix)

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Plots STRUCTURE analysis results (Q-matrix)

Description

This function takes a structure run object (output from gl.run.structure) and plots the typical structure bar plot that visualize the q matrix of a structure run.

Usage

gl.plot.structure(
  sr,
  K = NULL,
  met_clumpp = "greedyLargeK",
  iter_clumpp = 100,
  clumpak = TRUE,
  plot_theme = NULL,
  colors_clusters = NULL,
  ind_name = TRUE,
  border_ind = 0.15,
  plot.out = TRUE,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

sr	Structure run object from gl.run.structure [required].
K	The number for K of the q matrix that should be plotted. Needs to be within you simulated range of K's in your sr structure run object. If NULL, all the K's are plotted [default NULL].
met_clumpp	The algorithm to use to infer the correct permutations. One of 'greedy' or 'greedyLargeK' or 'stephens' [default "greedyLargeK"].
iter_clumpp	The number of iterations to use if running either 'greedy' 'greedyLargeK' [default 100].
clumpak	Whether use the Clumpak method (see details) [default TRUE].
plot_theme	Theme for the plot. See Details for options [default NULL].
colors_clusters	A color palette for clusters (K) or a list with as many colors as there are clusters (K) [default NULL].
ind_name	Whether to plot individual names [default TRUE].
border_ind	The width of the border line between individuals [default 0.25].
plot.out	Specify if plot is to be produced [default TRUE].
save2tmp	If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].
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]

Details

The function outputs a barplot which is the typical output of structure. For a Evanno plot use gl.evanno.

This function is based on the methods of CLUMPP and Clumpak as implemented in the R package starmie (https://github.com/sa-lee/starmie).

The Clumpak method identifies sets of highly similar runs among all the replicates of the same K. The method then separates the distinct groups of runs representing distinct modes in the space of possible solutions.

The CLUMPP method permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible.

This function averages the replicates within each mode identified by the Clumpak method.

Plots and table are saved to the temporal directory (tempdir) and can be accessed with the function gl.print.reports and listed with the function gl.list.reports. Note that they can be accessed only in the current R session because tempdir is cleared each time that the R session is closed.

Examples of other themes that can be used can be consulted in

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

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

Value

List of Q-matrices

Author(s)

Bernd Gruber & Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

References

• Pritchard, J.K., Stephens, M., Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.

• Kopelman, Naama M., et al. "Clumpak: a program for identifying clustering modes and packaging population structure inferences across K." Molecular ecology resources 15.5 (2015): 1179-1191.

• Mattias Jakobsson and Noah A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801-1806. Available at clumpp

See Also

gl.run.structure, gl.plot.structure

Examples

## Not run: 
#bc <- bandicoot.gl[,1:100]
#sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, exec = './structure')
#ev <- gl.evanno(sr)
#ev
#qmat <- gl.plot.structure(sr, K=3)
#head(qmat)
#gl.map.structure(qmat, K=3, bc, scalex=1, scaley=0.5)

## End(Not run)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.