plot.PLNPCAfit: PCA visualization (individual and/or variable factor map(s))...

In PLN-team/PLNmodels: Poisson Lognormal Models

PCA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

Description

PCA visualization (individual and/or variable factor map(s)) for a PLNPCAfit object

Usage

## S3 method for class 'PLNPCAfit'
plot(
  x,
  map = c("both", "individual", "variable"),
  nb_axes = min(3, x$rank),
  axes = seq.int(min(2, x$rank)),
  ind_cols = "ind_colors",
  var_cols = "var_colors",
  plot = TRUE,
  main = NULL,
  ...
)

Arguments

x	an R6 object with class PLNPCAfit
map	the type of output for the PCA visualization: either "individual", "variable" or "both". Default is "both".
nb_axes	scalar: the number of axes to be considered when map = "both". The default is min(3,rank).
axes	numeric, the axes to use for the plot when map = "individual" or map = "variable". Default it c(1,min(rank))
ind_cols	a character, factor or numeric to define the color associated with the individuals. By default, all variables receive the default color of the current palette.
var_cols	a character, factor or numeric to define the color associated with the variables. By default, all variables receive the default color of the current palette.
plot	logical. Should the plot be displayed or sent back as ggplot object
main	character. A title for the single plot (individual or variable factor map). If NULL (the default), an hopefully appropriate title will be used.
...	Not used (S3 compatibility).

Value

displays an individual and/or variable factor maps for the corresponding axes, and/or sends back a ggplot or gtable object

Examples

data(trichoptera)
trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
myPCAs <- PLNPCA(Abundance ~ 1 + offset(log(Offset)), data = trichoptera, ranks = 1:5)
myPCA <- getBestModel(myPCAs)
## Not run: 
plot(myPCA, map = "individual", nb_axes=2, ind_cols = trichoptera$Group)
plot(myPCA, map = "variable", nb_axes=2)
plot(myPCA, map = "both", nb_axes=2, ind_cols = trichoptera$Group)

## End(Not run)

PLN-team/PLNmodels documentation built on Oct. 13, 2024, 4:01 a.m.