utils.outflank.plotter: Plotting functions for Fst distributions after OutFLANK

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

Plotting functions for Fst distributions after OutFLANK

Description

This function takes the output of OutFLANK as input with the OFoutput parameter. It plots a histogram of the FST (by default, the uncorrected FSTs used by OutFLANK) of loci and overlays the inferred null histogram.

Usage

utils.outflank.plotter(
  OFoutput,
  withOutliers = TRUE,
  NoCorr = TRUE,
  Hmin = 0.1,
  binwidth = 0.005,
  Zoom = FALSE,
  RightZoomFraction = 0.05,
  titletext = NULL
)

Arguments

OFoutput	The output of the function OutFLANK()
withOutliers	Determines whether the loci marked as outliers (with $OutlierFlag) are included in the histogram.
NoCorr	Plots the distribution of FSTNoCorr when TRUE. Recommended, because this is the data used by OutFLANK to infer the distribution.
Hmin	The minimum heterozygosity required before including a locus in the plot.
binwidth	The width of bins in the histogram.
Zoom	If Zoom is set to TRUE, then the graph will zoom in on the right tail of the distirbution (based on argument RightZoomFraction)
RightZoomFraction	Used when Zoom = TRUE. Defines the proportion of the distribution to plot.
titletext	Allows a test string to be printed as a title on the graph

Value

produces a histogram of the FST

dartR documentation built on June 8, 2023, 6:48 a.m.