gl.plot.snmf: Plots ancestry coefficient from snmf

In dartR.popgen: Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Plots ancestry coefficient from snmf

Description

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

Usage

gl.plot.snmf(
  snmf.result,
  border.ind = 0.25,
  plot.K,
  plot.theme = NULL,
  color.clusters = NULL,
  ind.name = TRUE,
  plot.out = TRUE,
  plot.file = NULL,
  plot.dir = NULL,
  den = FALSE,
  inverse.den = TRUE,
  x = NULL,
  plot.colors.pop = gl.colors("dis"),
  verbose = 2
)

Arguments

snmf.result	run object from gl.run.snmf [required].
border.ind	The width of the border line between individuals [default 0.25].
plot.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 snmf run object [required].
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].
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].
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].
inverse.den	Flip dendrogram upside down [default TRUE].
x	The original genlight object used in gl.run.structure description [default NULL].
plot.colors.pop	A color palette for population plots or a list with as many colors as there are populations in the dataset [default gl.colors("dis")].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Details

The function outputs a barplot which is the typical output of snmf. Plots and table are saved to the working directory specified in plot.dir 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/

The Q matrices can be input to other R packages for plotting ancestry proportion, e.g. FSTruct https://github.com/MaikeMorrison/FSTruct

Value

Q-matrix

Author(s)

Ching Ching Lau (Post to https://groups.google.com/d/forum/dartr)

References

• Frichot E, Mathieu F, Trouillon T, Bouchard G, Francois O. (2014). Fast and Efficient Estimation of Individual Ancestry Coefficients. Genetics, 194(4): 973–983.

See Also

gl.run.snmf, gl.plot.snmf

Examples

# examples need LEA to be installed on the system (see above)
## Not run: 
m <- gl.run.snmf(x=bandicoot.gl, minK=1, 
maxK=5, rep=10)
Q <- gl.plot.snmf(snmf.result=m, plot.K = 3, ind.name=T)
gl.map.snmf(bandicoot.gl, qmat=Q)
# 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.snmf(bandicoot.gl, qmat=Q, movepops=mp)

## End(Not run)

dartR.popgen documentation built on March 16, 2026, 9:07 a.m.