alphaBetaPlot: Makes Alpha ~ Beta Plots for BGC results

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

Makes Alpha ~ Beta Plots for BGC results

Description

This function generates an Alpha x Beta 2D density plot with polygon hulls encapsulating alpha and beta outliers. 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

alphaBetaPlot(
  outlier.list,
  overlap.zero = TRUE,
  qn.interval = TRUE,
  both.outlier.tests = FALSE,
  saveToFile = NULL,
  plotDIR = "./plots",
  showPLOTS = FALSE,
  device = "pdf",
  neutral.color = "gray",
  alpha.color = "blue",
  beta.color = "red",
  both.color = "purple",
  margins = c(150, 5.5, 5.5, 5.5),
  margin.units = "points",
  padding = 0.1,
  height = 7,
  width = 7,
  dim.units = "in",
  text.size = 18,
  dpi = 300,
  alpha_limits = NULL,
  beta_limits = NULL
)

Arguments

outlier.list	List of data.frames returned from get_bgc_outliers(). see ?get_bgc_outliers for more info
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
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"
alpha.color	Color for alpha outlier loci. Default = "blue"
beta.color	Color for beta outlier loci. Default = "red"
both.color	Color for loci that are 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"
padding	Padding to add to X and Y axes. Default=0.1
height	Height for plot. Default = 7
width	Width for plot. Default = 7
dim.units	Units for height and width. Default = "in"
text.size	Size for plot text. Default = 18
dpi	DPI for saving plot. Default = 300
alpha_limits	Limits (e.g., c(1,1) for plotting alpha. Default = NULL
beta_limits	Limits (e.g., c(1,1) for plotting beta. Default = NULL
line.size	Size of regression lines in plot. Default = 0.25

Details

Generates Alpha x Beta Density Plots, Highlighting Outliers.

Examples

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

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

phiPlot(outlier.list = full.outliers,  overlap.zero = FALSE)

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