diallelPlotter: DIDACT grid plot of posterior utility.

In gkeele/DIDACT: Diallel Informed Decision theoretic Approach for Crosses Tool (DIDACT)

Description

This function takes posterior samples of utilities from evaluate.experiments() and produces a grid plot of the posterior utilities for specified cross type.

Usage

diallelPlotter(results, utility.type = c("power", "contrasts"),
  cross.type = c("f2", "bc", "rbc1", "rbc2"), pheno.name = "",
  col.range = c("white", "black"), col.spectrum = c("blue2red", "gray",
  "green2red", "blue2green"), path = NULL, height = 12, width = 12,
  strains.relabel = NULL, include.off.x = TRUE,
  include.letter.labels = TRUE, include.asterisk.labels = FALSE,
  include.density = TRUE, include.var.pie = FALSE,
  include.bar.plots = TRUE, density.col = "white",
  border.col = "black", median.line.col = "black",
  absolute.density.scale = TRUE, include.info.plot = TRUE,
  include.rank = FALSE, rank = NULL, rank.col = "red",
  label.cex = 1.1, label.padj = -0.3, ...)

Arguments

results	Samples of posterior utility produced by evaluate.experiments().
utility.type	DEFAULT: "power". The posterior utility to be plotted. Currently the options are "power" and "contrasts". Power is more appropriate for Mendelian-like phenotypes. Contrasts make less assumptions.
cross.type	DEFAULT: "f2". Current options include "f2", "bc", "rbc1", and "rbc2".
pheno.name	DEFAULT: "". Included in the information panel.
col.range	DEFAULT: c("white", "black"). If specified, will create a color spectrum scale between the two colors included.
col.spectrum	DEFAULT: "blue2red". Use pre-specified spectrum. Options include "blue2red", "gray", "green2red", and "blue2green".
path	DEFAULT: NULL. If a path is specified, a pdf will be created.
height	DEFAULT: 12. The height of the pdf in inches.
width	DEFAULT: 12. The width of the pdf in inches.
strains.relabel	DEFAULT: NULL. Option to re-label the strains.
include.off.x	DEFAULT: TRUE. If TRUE, "X" is plotted on the diagonal and lower diagonal of the grids. If FALSE, square is left empty.
include.letter.labels	DEFAULT: TRUE. If TRUE, letters are included to indicate backcross parent.
include.asterisk.labels	DEFAULT: FALSE. If TRUE, asterisks are included to signify backcross parent.
include.density	DEFAULT: TRUE. If TRUE, histogram of posterior density is included in square.
include.var.pie	DEFAULT: FALSE. If TRUE, pie chart of phenotypic variance is included in square.
include.bar.plots	DEFAULT: TRUE. If TRUE, box plots of posterior genotype class phenotypes are included in square.
density.col	DEFAULT: "white". The color of the histogram if included in square.
border.col	DEFAULT: "black". The color of the border lines of the various figures.
median.line.col	DEFAULT: "black". The color of the vertical line that marks the median utility.
absolute.density.scale	DEFAULT: TRUE. If TRUE, the densities are scaled to the same height.
include.info.plot	DEFAULT: TRUE. If TRUE, info plot is included in one of the diagonal squares.
include.rank	DEFAULT: FALSE. If TRUE, the rank of mean posterior utility is included on the cross square.
rank.col	DEFAULT: "red". The color of the rank index included on the square.
label.cex	DEFAULT: 1.1. Specifies the size of the strain labels.
label.padj	DEFAULT: -0.3. Specifies how much the strain label is shifted from the square.

Examples

diallelPlotter()

gkeele/DIDACT documentation built on Jan. 1, 2020, 2:58 a.m.