plotFASTA: Plot the different nucleotides present in an alignment of...
In JosephCrispell/plotteR: A collection of functions to help with base R plotting

Function uses coloured polygons to illustrate which nucleotides are present in each sequence at each position

plotFASTA(
  nucleotideAlignment,
  pdfFileName = NULL,
  pdfWidth = 14,
  pdfHeight = 7,
  labelSpace = 1,
  lineForSequenceNames = 0,
  sequenceLabelCex = 0.5,
  xLabCex = 1,
  xTicksCex = 1,
  legendCex = 1,
  showNucleotide = FALSE,
  removeUninformative = FALSE
)

`nucleotideAlignment`	A matrix or a list containing the DNA sequences, or an object of class "alignment", "phyDat", or "DNAbin"
`pdfFileName`	A character string providing the name of a PDF to send plot into. Default value is NULL (plot not sent to file)
`pdfWidth`	The width of the graphics region in inches. Default value is 14.
`pdfHeight`	The height of the graphics region in inches. Default value is 7.
`labelSpace`	Numeric multiplier to change the size of the space alotted to the sequence labels
`lineForSequenceNames`	The number of lines into the margin at which the sequence names will be plotted. Default value is 0.
`sequenceLabelCex`	Numeric multiplier to change the size of the sequence labels. Default value is 0.5.
`xLabCex`	Numeric multiplier to change size of X axis label. Default value is 1.
`xTicksCex`	Numeric multipler to change size of X axis tick labels. Default value is 1.
`legendCex`	Numeric multiplier to change size of legend (points and text). Default value is 1.
`showNucleotide`	Boolean flag to decide whether or not to plot nucleotide characters onto figure. Defaults to off.
`removeUninformative`	Boolean flag to decide whether to remove sites where all sequences have the same allele. Default is `FALSE`.

# Create an example dataset
nSequences <- 50
nSites <- 100
alignment <- matrix(sample(c("A", "C", "G", "T"), nSequences*nSites, replace=TRUE),
                    nrow=nSequences, ncol=nSites)
rownames(alignment) <- paste("Seq-", 1:nSequences)

# Plot the FASTA
plotFASTA(alignment, xTicksCex = 1.5, xLabCex=1.5, sequenceLabelCex=0.4)