plot_mzxml_boxplot: Make a boxplot out of some of the various data available in...

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

Make a boxplot out of some of the various data available in the mzxml data.

Description

There are a few data within the mzXML raw data files which are likely candidates for simple summary via a boxplot/densityplot/whatever. For the moment I am just doing boxplots of a few of them. Since my metadata extractor dumps a couple of tables, one must choose a desired table and column from it to plot.

Usage

plot_mzxml_boxplot(
  mzxml_data,
  table = "precursors",
  column = "precursorintensity",
  violin = FALSE,
  names = NULL,
  plot_title = NULL,
  scale = NULL,
  ...
)

Arguments

mzxml_data	Provide a list of mzxml data, one element for each sample.
table	One of precursors or scans
column	One of the columns from the table; if 'scans' is chosen, then likely choices include: 'peakscount', 'basepeakmz', 'basepeakintensity'; if 'precursors' is chosen, then the only likely choice for the moment is 'precursorintensity'.
violin	Print the samples as violins rather than only box/whiskers?
names	Names for the x-axis of the plot.
plot_title	Title the plot?
scale	Put the data on a specific scale?
...	Further arguments, presumably for colors or some such.

Value

Boxplot describing the requested column of data in the set of mzXML files.

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