agricolae (version 1.2-8)

plot.AMMI: PLOT AMMI

Description

Biplot AMMI.

Usage

# S3 method for AMMI
plot(x,first=1,second=2,third=3,type=1,number=FALSE,gcol=NULL,ecol=NULL,
icol=NULL,angle=25,lwd=1.8,length=0.1,xlab=NULL,ylab=NULL,xlim=NULL,ylim=NULL,...)

Arguments

x

object AMMI

first

position axis x, 0=Y-dependent, 1=PC1, 2=PC2, 3=PC3

second

position axis y,0=Y-dependent, 1=PC1, 2=PC2, 3=PC3

third

position axis z,0=Y-dependent, 1=PC1, 2=PC2, 3=PC3

type

1=biplot, 2= triplot 3=influence genotype

number

TRUE or FALSE names or number genotypes

gcol

genotype color

ecol

environment color

icol

influence color

angle

angle from the shaft of the arrow to the edge of the arrow head

lwd

parameter line width in function arrow

length

parameter length in function arrow

xlab

x labels

ylab

y labels

xlim

x limites

ylim

y limites

…

other parameters of plot

Details

type=1 produce graphs biplot. type=2 produce graphs triplot, the components are normalizad in scale 0-1. type=3 produce graphs on a 2d point set that are all subgraphs of the Delaunay triangulation with relative neighbor graph.

The relative neighbor graph is defined by the relation, x and y are neighbors if

$$d(x,y) \le min(max(d(x,z),d(y,z))| z \in S)$$

where d() is the distance, S is the set of BIPLOT points and z is an arbitrary point in S.

help(relativeneigh) package=spdep

See Also

AMMI

Examples

# NOT RUN {
library(agricolae)
data(plrv)
model<- with(plrv,AMMI(Locality, Genotype, Rep, Yield))
# biplot PC2 vs PC1
plot(model)
## plot PC1 vs Yield
plot(model,0,1,gcol="blue",ecol="green")
## triplot PC 2,3,4
if (requireNamespace("klaR", quietly = TRUE)) {
plot(model,first=2,second=3,third=4, type=2,number=TRUE)
}
# biplot with influence genotype in pc3 vs pc2
if (requireNamespace("spdep", quietly = TRUE)) {
plot(model,first=2,second=3, type=3,number=TRUE,icol="green")
}
# }

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