plot_spectra_peaks: Plot only the Peaks in a spectra matrix

In krisrs1128/phyloseqExtend: Extend Phyloseq to Rich Data Types

Description

Plot only the Peaks in a spectra matrix

Usage

plot_spectra_peaks(physeq, 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,
  ...)

Arguments

physeq	A phyloseq object containing the spectrum to plot
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.

Value

p The ggplot object containing plots of the raw spectra, with color / linetype / faceting annotation as desired.

krisrs1128/phyloseqExtend documentation built on May 20, 2019, 1:31 p.m.