gl.plot.structure {dartR.popgen}

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,
  color_clusters = NULL,
  ind_name = TRUE,
  k_name = NULL,
  border_ind = 0.15,
  den = FALSE,
  dis.mat = NULL,
  x = NULL,
  plot.out = TRUE,
  plot.file = NULL,
  plot.dir = NULL,
  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].

color_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].

k_name

Name of the structure plot to plot. It should be character [default NULL].

border_ind

The width of the border line between individuals [default 0.25].

den

Whether to include a dendrogram. It is necessary to include the original genlight object used in gl.run.structure in the parameter x [default FALSE].

dis.mat

A dis object (distance matrix) to be used to order structure plot which is plotted together with structure plot [default NULL].

x

The original genlight object used in gl.run.structure description [default NULL].

plot.out

Specify if plot is to be produced [default TRUE].

plot.file

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

plot.dir

Directory in which to save files [default = working directory]

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 working directory specified in plot.dir (tempdir ) if plot.file is set.

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

# examples need structure to be installed on the system (see above)
## 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)