predict_PCA: PCA plots

In adamd3/codondiffR: Codon usage comparisons across taxa

PCA plots

Description

Predict taxonomic classifications for sequences in a codonFreq) object, using linear discriminants from an PCA) model. Plot disciminants and predictions.

Usage

predict_PCA(
  cFobj,
  pcaObj,
  rank = "Phylum",
  minlen = 600,
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  norm = FALSE,
  save = FALSE,
  identifier = NULL,
  includeTax = NULL,
  colours = NULL
)

## S4 method for signature 'codonFreq'
predict_PCA(
  cFobj,
  pcaObj,
  rank,
  minlen,
  fname,
  units,
  width,
  height,
  dpi,
  norm,
  save,
  identifier,
  colours
)

Arguments

cFobj	An object of class codonFreq.
pcaObj	Object of class prcomp.
rank	Character, taxonomic rank to be used for categorisation. Options are "Domain", "Kingdom", and "Phylum". Default = "Phylum".
minlen	Numeric, the minimum length of sequence (in codons) to be included in the analysis. Default = 500.
fname	Character, name of figure generated.
units	Numeric, units to be used for defining the plot size. Options are "in" (default), "cm", and "mm".
width	Numeric, width of the figure (in units).
height	Numeric, height of the figure (in units).
dpi	Numeric, resolution of the figure (default = 600).
norm	Logical, should the codon abundances be normalised? If TRUE, codon abundances will be converted to codon bias scores, such that the sum of scores for each amino acid sum to 1. Default = FALSE.
save	Logical, should the enrichment results plot be saved to a file? Default = FALSE.
identifier	Character, optional group label to be assigned to sequences in the codonFreq object. If not supplied, each sequence will be labelled individually on the plot. Maximum number of unique identifiers = 6.
includeTax	Character, optional vector of taxa (at the specified rank) to be included in the PCA. If not supplied, all taxa will be used.
colours	Integer vector, containing values between 1 and 9, which specifies the colours to be used from the 'Set1' palette in the 'RColorBrewer' package.

Value

A ggplot object.

Examples

    virusSet <- readSeq(example = TRUE)
    virusCF <- codonFreq(virusSet)
    exclCod <- c("ATT", "TGT")
    PCA_tmp <- PCA(exclude = exclCod, rank = "Phylum", minlen = 600)
    predPCA <- predict_PCA(
        virusCF, PCA_tmp, rank = "Phylum", save = TRUE,
        minlen = 600, fname = "PCA_tmp2", height = 5, width = 7
    )

adamd3/codondiffR documentation built on Sept. 3, 2022, 2:26 a.m.