MultANOVA (version 1.0.1)

plot.DCDA: Plots for DCDA objects

Description

Plots results from DCDA with possible customizations from the different arguments.

Usage

# S3 method for DCDA
plot(
  x,
  axes = c(1, 2),
  pair.comp = NULL,
  alpha = 0.05,
  select.var = 1:nrow(x$var.coord),
  select.level = 1:nrow(x$level.coord),
  title = NULL,
  size = 2.25,
  expansion.var = 1.25,
  ...
)

Value

The required plot.

Arguments

x

An object resulting from DCDA.

axes

Which dimensions should be plotted?

pair.comp

An optional objects resulting from MultLSD. When provided, no discriminated modalities of the factor at the alpha risk will linked on the plot.

alpha

The alpha risk to determine evaluate significance of the p-values from pair.comp.

select.var

The indices of the variables to be plotted. By default all variables are plotted.

select.level

The indices of the levels of the term to be plotted. By default all levels of the term are plotted.

title

An optional character specifying a title for the plot.

size

The overall size of labels, points, etc.

expansion.var

The factor of expansion applied to variables coordinates to increase readability

...

further arguments passed to or from other methods.

Examples

data(OTU)
acd=DCDA(~Lot+Atm+Time,OTU[,1:4],OTU[,-c(1:4)],"Time")
lsd=MultLSD(~Lot+Atm+Time,OTU[,1:4],OTU[,-c(1:4)],"Time")
fish=FisherS(~Lot+Atm+Time,OTU[,1:4],OTU[,-c(1:4)],"Time")
plot(acd,axes = c(1,2),pair.comp = lsd,expansion.var = 1.5,select.var = which(fish[2,]<=0.05))