plot_intensity_mz: Plot mzXML peak intensities with respect to m/z.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Plot mzXML peak intensities with respect to m/z.

Description

I want to have a pretty plot of peak intensities and m/z. The plot provided by this function is interesting, but suffers from some oddities; notably that it does not currently separate the MS1 and MS2 data.

Usage

plot_intensity_mz(
  mzxml_data,
  loess = FALSE,
  alpha = 0.5,
  ms1 = TRUE,
  ms2 = TRUE,
  x_scale = NULL,
  y_scale = NULL,
  ...
)

Arguments

mzxml_data	The data structure from extract_mzxml or whatever it is.
loess	Do a loess smoothing from which to extract a function describing the data? This is terribly slow, and in the data I have examined so far, not very helpful, so it is FALSE by default.
alpha	Make the plotted dots opaque to this degree.
ms1	Include MS1 data in the plot?
ms2	Include MS2 data in the plot?
x_scale	Plot the x-axis on a non linear scale?
y_scale	Plot the y-axis on a non linear scale?
...	Extra arguments for the downstream functions.

Value

ggplot2 goodness.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.