gl.smearplot: Smear plot

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

Smear plot

Description

Each locus is color coded for scores of 0, 1, 2 and NA for SNP data and 0, 1 and NA for presence/absence (SilicoDArT) data. Individual labels can be added. Plot may become cluttered if ind.labels If there are too many individuals, it is best to use ind.labels = FALSE.

Works with both SNP data and P/A data (SilicoDArT)

Usage

gl.smearplot(
  x,
  plot.display = TRUE,
  ind.labels = FALSE,
  label.size = 10,
  group.pop = FALSE,
  plot.theme = NULL,
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  het.only = FALSE,
  legend = "bottom",
  verbose = NULL
)

Arguments

x	Name of the genlight object [required].
plot.display	If TRUE, the plot is displayed in the plot window [default TRUE].
ind.labels	If TRUE, individual IDs are shown [default FALSE].
label.size	Size of the individual labels [default 10].
group.pop	If ind.labels is TRUE, group by population [default TRUE].
plot.theme	Theme for the plot. See Details for options [default NULL].
plot.colors	List of four color names for the column fill for homozygous reference, heterozygous, homozygous alternate, and missing value (NA) [default c("#0000FF","#00FFFF","#FF0000","#e0e0e0")].
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()]#'
het.only	If TRUE, show only the heterozygous state [default FALSE]
legend	Position of the legend: “left”, “top”, “right”, “bottom” or 'none' [default = 'bottom'].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Value

Returns the ggplot object

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

Other graphics: gl.colors(), gl.map.interactive(), gl.plot.heatmap(), gl.report.ld.map(), gl.select.colors(), gl.select.shapes(), gl.tree.nj()

Examples

gl.smearplot(testset.gl,ind.labels=FALSE)
gl.smearplot(testset.gs,ind.labels=FALSE)
gl.smearplot(testset.gl[1:10,],ind.labels=TRUE)
gl.smearplot(testset.gs[1:10,],ind.labels=TRUE)

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