plot_spectra: Plot Spectra Intensities
In krisrs1128/phyloseqExtend: Extend Phyloseq to Rich Data Types

Description Usage Arguments Value

If spectra(physeq)[["peaks"]] is FALSE, then this will plot the raw intensities of each spectrum in the sample. Otherwise, we only plot the positions and heights of peaks for each sample.

plot_spectra(physeq, method = "speaq", plot_type = "specmat",
  log_scale = FALSE, subsample_frac = 1, x_min = NULL, x_max = NULL,
  col = NULL, linetype = NULL, facet_cols = NULL, plot_title = NULL,
  alpha = 1, line_thickness = 1, ...)

`physeq`	A phyloseq object containing the spectrum to plot
`method`	The R package to use for the plot. Currently only supports "speaq" or "ggplot2".
`log_scale`	Should the intensities be plotted on a log scale?
`subsample_frac`	We will only plot ever the value at every 1 / subsample_frac indices. This can accelerate plotting in the case that
`x_min`	What is the minimum index to display?
`x_max`	What is the maximum index to display?
`col`	A string giving a column name in sample_data(physeq) according to which we will color the spectra.
`linetype`	A string giving a column name in sample_data(physeq) according to which we will modify the spectra linetypes.
`facet_cols`	A character vector giving the column names in sample_data(physeq) according to which to facet the plot by.
`plot_title`	A title to include for the figure.
`alpha`	The transparency parameter for the plots, when using ggplot2.
`line_thickness`	The thickness of the spectra lines, when using ggplot2.