phiPlot: Makes Phi ~ Hybrid Index Plots for Alpha and Beta

In btmartin721/ClineHelpR: Parses and Plots BGC and INTROGRESS Output

Makes Phi ~ Hybrid Index Plots for Alpha and Beta

Description

This function generates the Phi ~ Hybrid Index genomic cline plot shown in Gompert et al. (2012). Outlier genomic clines are colored black, whereas non-outliers are gray. Phi is the Prob. Ancestry for P1. 1-Phi = P(P0 ancestry). The plot can be printed to the plot window in Rstudio (default) or saved to file by specifying a file prefix with the saveToFile option.

Usage

phiPlot(
  outlier.list,
  popname = "Population 1",
  overlap.zero = TRUE,
  qn.interval = TRUE,
  both.outlier.tests = FALSE,
  line.size = 0.25,
  saveToFile = NULL,
  plotDIR = "./plots",
  showPLOTS = FALSE,
  device = "pdf",
  neutral.color = "gray",
  neutral.line.color = "black",
  neutral.line.size = 1,
  zero.line = TRUE,
  zero.linetype = "dashed",
  alpha.color = "blue",
  beta.color = "red",
  both.color = "purple",
  margins = c(150, 5.5, 5.5, 5.5),
  margin.units = "points",
  phi.height = 7,
  phi.width = 7,
  phi.units = "in",
  phi.text.size = 18,
  phi.dpi = 300,
  hist.height = 1.5,
  hist.width = 1,
  hist.x.origin = 0,
  hist.y.origin = 1.05,
  hist.color = "gray57",
  hist.fill = "gray57",
  hist.axis.text.size = 12,
  hist.axis.title.size = 12,
  hist.binwidth = 0.1
)

Arguments

outlier.list	List of data.frames returned from get_bgc_outliers(). see ?get_bgc_outliers for more info
popname	Population name to use as the plot title
overlap.zero	Boolean. If TRUE, outliers include when the credible doesn't contain 0
qn.interval	Boolean. If TRUE, outliers = outside quantile interval
both.outlier.tests	If TRUE, outliers = both overlap.zero and qn.interval
line.size	Size of regression lines in plot. Default = 0.25
saveToFile	If specified, saves plots to file. The value for saveToFile should be the prefix for the filename you want to save to
plotDIR	Directory path. If saveToFile is specified, plots are saved in this directory
showPLOTS	Boolean Whether to print the plots to the screen
device	File format to save plot. Supports ggplot2::ggsave devices
neutral.color	Color for non-outlier loci. Default = "gray"
neutral.line.color	Color for dashed linear line showing mean Default = "black"
neutral.line.size	Size for dashed linear line showing mean. Default = 1.0
zero.line	Boolean to include linear line for alpha=0 and beta=0. Default = TRUE
zero.linetype	Character string to set linetype for zero.line. Default = "dashed"
alpha.color	Color for alpha outlier loci. Default = "blue"
beta.color	Color for beta outlier loci. Default = "red"
both.color	Color for SNPs that are both alpha and beta outliers. Default = "purple"
margins	Vector of margins for phi plot: c(Top, Right, Bottom, Left) Top is extended to include the Hybrid Index histogram
margin.units	Units for margins parameter. Default = "points"
phi.height	Height for Phi plot. Default = 7
phi.width	Width for Phi plot. Default = 7
phi.units	Units for phi height and width. Default = "in"
phi.text.size	Size for Phi plot text. Default = 18
phi.dpi	DPI for saving Phi plot. Default = 300
hist.height	Height of Hybrid Index histogram in Phi data coordinates E.g., If you want the histogram to be equal to half the height of the phi plot, set hist.height to 0.5
hist.width	Height of Hybrid Index histogram in Phi data coordinates E.g., If you want the histogram to be the same width as the Phi plot, set this to 1.0
hist.x.origin	X Origin (in Phi data coordinates) for Hybrid Index histogram
hist.y.origin	Y origin (in Phi data coordinates) for Hybrid Index histogram. Set to just above the Phi plot by default
hist.color	Color of Hybrid Index histogram
hist.fill	Fill for Hybrid Index histogram
hist.axis.text.size	Text size for histogram x-axis
hist.axis.title.size	Title size for histogram x-axis
hist.binwidth	Binwidth for Hybrid Index histogram

Details

Calculates Phi and Plots Phi ~ Hybrid Index, Highlighting Outliers.

Examples

phiPlot(outlier.list = outliers, saveToFile = "pop1_phiPlot",
plotDIR = "./bgc_plots", device = "png")

phiPlot(outlier.list = gene.outliers, popname = "Mus musculus",
line.size = 0.1, qn.interval = FALSE, overlap.zero = FALSE,
both.outlier.tests = TRUE, saveToFile = "mus_phiPlot")

phiPlot(outlier.list = full.outliers, popname = "G. gorilla",
overlap.zero = FALSE)

btmartin721/ClineHelpR documentation built on Oct. 15, 2024, 5:05 a.m.