BBplot: BBplot function

Description Usage Arguments Details Examples

View source: R/BBplot.R

Description

This function makes biplots from a bilinear() object

Usage

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BBplot(bilinearObject, f = 0.5, pdf.filename = NULL, nPC = NULL,
  plottitle = "Biplot", biplot3D = FALSE, outer.box = TRUE,
  internal.axes = FALSE, scaled = TRUE, decorateGGE = FALSE,
  Gnames = TRUE)

Arguments

bilinearObject

object from output of a call to biliner()

f

numeric. Scale parameter in (0, 1) for exponent on eigenvalues for weighting the genotype scores. Environment scores are weighted 1 - f. Default is 0.5

pdf.filename

name of pdf file to output. If NULL, biplot is printed to default device.

nPC

integer. Number of principal components to graph in the model. Default is 2 for a 2D biplot and 3 for a 3D biplot. If the number of significant PCs is less than the default and no argument is provided to 'nPC', the mean will be printed on the x axis, and the 1st (or 1st and 2nd for 3D biplot) PC will be printed on the remaining axis(es)

plottitle

character. Title for biplot.

biplot3D

logical. Should a 3dimensional

outer.box

logical. Shoudl a box be printed around the plot. default is TRUE.

internal.axes

logical. For 3D biplots(?) default is FALSE

scaled

logical. default is TRUE

decorateGGE

logical. should a GGE plot be decorate to dilineate megaenvironments to determine genotype winners?

Gnames

character vector of genotype names to be included on plot near respective points

Details

put some details here

Examples

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data(soy)
AMMIfit <- bilinear(x = soyShort)
AMMIplot(AMMIfit)
AMMIplot(AMMIfit, "winner")
AMMIplot(AMMIfit, "winner", color = "hotpink")
AMMIplot(AMMIfit, c("linear", "winner"), color = c("hotpink", "darkorchid"))

data(onterio)
GGEfit <- bilinear(x = onterio, model = "GGE")
BBplot(GGEfit, decorateGGE = TRUE)

nsantantonio/Bilinear documentation built on Dec. 7, 2017, 5:45 a.m.