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

plot.PLNPCAfit {PLNmodels}

R Documentation

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)