plot: highlightR plotting
In PoonLab/highlineR: A Novel Visualization Tool to Assess Diversity in NGS Data

Description Usage Arguments Value

Plots highlineR Data objects.

## S3 method for class 'session'
plot(x, mode = "mismatch", master, sort_by, rf = 1,
  use_sample = T, ...)

## S3 method for class 'Data'
plot(x, session_plot = F, mode = "mismatch",
  master = x$master, sort_by = "similarity", rf = 1,
  use_sample = T, ...)

`x`	Data object or session object containing Data objects to plot.
`mode`	A character string representing the desired mutation annotation for plotting. Options: "mismatch" (default), "svn" (Synonymous versus Non-Synonymous), "tvt" (Transition versus Transversion).
`master`	A character string representing the sequence to which other sequences should be compared. By default, the most abundant sequence is selected.
`sort_by`	A character string representing how the sequences should be ordered in a plot. Options: "similarity", "frequency".
`rf`	An integer specifying which reading frame should be used when determining Synonymous vs Non-Synonymous mutations. Options: 1 (default), 2, 3.
`use_sample`	A logical value specifying which environment should be plotted. If `True`, then the `sample` environment of the Data objects is plotted. If `False`, the complete `compressed` environment is plotted.
`seq_diff`	matrix of compositional differences between sequences.
`seq_order`	string vector of sequences present in compressed environment ordered as desired for plotting.