plots: LDA plots

In adamd3/codondiffR: Codon usage comparisons across taxa

LDA plots

Description

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

Plot the distribution of MCUFD values per taxon

Usage

## S4 method for signature 'codonFreq'
predict_LDA(
  cFobj,
  ldaObj,
  rank = "Phylum",
  minlen = 600,
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  norm = FALSE,
  plot = FALSE,
  identifier = NA_character_
)

## S4 method for signature 'list'
MCUFD_plot(
  cFres,
  type = "bar",
  n = NA_real_,
  rank = "Phylum",
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  save = FALSE
)

Arguments

cFobj	An object of class codonFreq.
ldaObj	Object of class lda - produced using the lda() function.
rank	Character, taxonomic rank to be used for categorisation of the CUFD hit sequences. 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.
plot	Logical, should the enrichment results be plotted? 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.
cFres	List of data frames containing MCUFD results.
type	Character, the type of plot to make. Options are "bar" (default) and "line".
n	Numeric, the number of top-ranked reference taxa to be plotted per input sequence. Default = 100.
save	Logical, should the figure be saved to file? Default = FALSE.

Value

A ggplot object.

A ggplot object.

Examples

   virusSet <- readSeq(example = TRUE)
   virusCF <- codonFreq(virusSet)
    exclCod <- c("ATT", "TGT")
    LDA_tmp <- LDA(
        exclude = exclCod, rank = "Phylum", trans = FALSE,
        propTrain = 1, corCut = 0.95, minlen = 600
    )
    predLDA <- predict_LDA(
        virusCF, LDA_tmp, rank = "Phylum", plot = TRUE,
        minlen = 600, fname = "lda_tmp2", height = 5, width = 7
    )
    head(sort(table(predLDA$class), decreasing = TRUE))

   virusSet <- readSeq(example = TRUE)
   virusCF <- codonFreq(virusSet)
   exclCod <- c("ATT", "TGT")
   MCUFD_tmp <- MCUFD(virusCF, exclude = exclCod, norm = TRUE)
   MCUFD_plot(
       cFres = MCUFD_tmp, type = "bar", save = TRUE,
       fname = "MCUFD_bar_kingdom", n = 100, rank = "Kingdom"
   )

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