plot_raw_spectra: Plot Raw Spectra Intensities Across All Indices
In krisrs1128/phyloseqExtend: Extend Phyloseq to Rich Data Types

Description Usage Arguments Value

Before preprocessing to a collection of peaks, it may be useful to plot the full raw spectra. This function provides an interface to speaq and ggplot2 that can be used to plot these raw spectra.

plot_raw_spectra(physeq, method = "speaq", 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 the spectrum is very long, but can lead to missed peaks.
`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.