runtess: Run tess3r and plot results Pipeline with wrappers for...

In JeffWeinell/misc.wrappers: Miscellaneous Wrapper Functions for Spatial Population Genomics

Run tess3r and plot results Pipeline with wrappers for several functions from the tess3r package. Data can be supplied as a VCF file and results are plotted in multiple useful ways.

Description

Run tess3r and plot results

Pipeline with wrappers for several functions from the tess3r package. Data can be supplied as a VCF file and results are plotted in multiple useful ways.

Usage

runtess(
  x,
  format = "VCF",
  coords,
  samplenames = NULL,
  kmax = 10,
  reps = 30,
  save.in = NULL,
  mask = 0.05,
  max.iteration = 500,
  include.out = c(".pdf", ".Qlog", ".entropyLog"),
  overwrite = FALSE
)

Arguments

x	'vcfR' object (see package::vcfR) or character string with path to SNPs dataset fornatted to match the 'format' argument. Currently only VCF can be used, but others may be added soon.
format	Character string indicating the format of the data. Currently only "VCF" or "fastStructure" allowed. Other types may be added. Ignored if x is a vcfR object.
coords	Either a character string with path to file containing coordinates (longitude in first column, latitude in second column), or matrix object with longitude and latitude columns.
samplenames	NULL or a character string vector with names of samples (in same order) as data in x and coords. If NULL (the default), sample names are extracted from x.
kmax	Numerical vector with set of values to use for K. Default 40.
reps	Number of repititions. Default 100.
save.in	Where to save output files. Default is NULL.
mask	Proportion of input data to mask during each replicate when tess3 function is called. Default 0.05.
max.iteration	Max iterations. Default 500.
include.out	Character vector indicating which type of files should be included as output. Default is c(".pdf",".Qlog", and ".entropyLog").
overwrite	Logical indicating whether or not to allow new output files to overwrite existing ones. Default FALSE.

Value

List of plots

JeffWeinell/misc.wrappers documentation built on Sept. 20, 2023, 12:42 p.m.