gl.map.structure: Maps a STRUCTURE plot using a genlight object

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

Maps a STRUCTURE plot using a genlight object

Description

This function takes the output of plotstructure (the q matrix) and maps the q-matrix across using the population centers from the genlight object that was used to run the structure analysis via gl.run.structure) and plots the typical structure bar plots on a spatial map, providing a barplot for each subpopulation. Therefore it requires coordinates from a genlight object. This kind of plots should support the interpretation of the spatial structure of a population, but in principle is not different from gl.plot.structure

Usage

gl.map.structure(
  qmat,
  x,
  K,
  provider = "Esri.NatGeoWorldMap",
  scalex = 1,
  scaley = 1,
  movepops = NULL,
  pop.labels = TRUE,
  pop.labels.cex = 12
)

Arguments

qmat	Q-matrix from a structure run followed by a clumpp run object [from gl.run.structure and gl.plot.structure] [required].
x	Name of the genlight object containing the coordinates in the \@other$latlon slot to calculate the population centers [required].
K	The number for K to be plotted [required].
provider	Provider passed to leaflet. Check providers for a list of possible backgrounds [default "Esri.NatGeoWorldMap"].
scalex	Scaling factor to determine the size of the bars in x direction [default 1].
scaley	Scaling factor to determine the size of the bars in y direction [default 1].
movepops	A two-dimensional data frame that allows to move the center of the barplots manually in case they overlap. Often if populations are horizontally close to each other. This needs to be a data.frame of the dimensions [rows=number of populations, columns = 2 (lon/lat)]. For each population you have to specify the x and y (lon and lat) units you want to move the center of the plot, (see example for details) [default NULL].
pop.labels	Switch for population labels below the parplots [default TRUE].
pop.labels.cex	Size of population labels [default 12].

Details

Creates a mapped version of structure plots. For possible background maps check as specified via the provider: http://leaflet-extras.github.io/leaflet-providers/preview/index.html. You may need to adjust scalex and scaley values [default 1], as the size depends on the scale of the map and the position of the populations.

Value

An interactive map that shows the structure plots broken down by population.

returns the map and a list of the qmat split into sorted matrices per population. This can be used to create your own map.

Author(s)

Bernd Gruber (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.

• Archer, F. I., Adams, P. E. and Schneiders, B. B. (2016) strataG: An R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour. doi:10.1111/1755-0998.12559

• Evanno, G., Regnaut, S., and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14:2611-2620.

• 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, clumpp, 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.exe')
#ev <- gl.evanno(sr)
#ev
#qmat <- gl.plot.structure(sr, k=2:4)#' #head(qmat)
#gl.map.structure(qmat, bc,K=3)
#gl.map.structure(qmat, bc,K=4)
#move population 4 (out of 5) 0.5 degrees to the right and populations 1
#0.3 degree to the north of the map.
#mp <- data.frame(lon=c(0,0,0,0.5,0), lat=c(-0.3,0,0,0,0))
#gl.map.structure(qmat, bc,K=4, movepops=mp)

## End(Not run)

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