MS Data Analysis

This function takes an MSnExp object and plots a 2D chromatogram using the specified modulation time and optional ion extraction. The function relies on ggplot2 for plotting.

plot2D(
  object,
  file = 1,
  mod.time,
  delay.time = 0,
  ion = NULL,
  mz.tol = c("ppm", "abs"),
  ppm.tol = 20,
  abs.tol = 0.5,
  log.scale = F,
  rt.min = 0,
  rt.max = max(rtime(object)),
  rt2.min = 0,
  rt2.max = mod.time,
  mz.min = min(object@featureData$lowMZ),
  mz.max = max(object@featureData$highMZ),
  int.min = 0,
  int.max = max(tic(object), na.rm = T) + 1,
  color.scale = "Spectral",
  reverse.scale = T,
  save.output = F,
  filename = "2dplot",
  filetype = ".pdf",
  filepath = ".",
  print.output = T,
  mz.digits = 4,
  plot.type = c("2D", "2Di", "3D")
)

`object`	An MSnExp object
`file`	Which file (numeric, not filename) to pull data from. Default is 1
`mod.time`	The modulation time of the 2D run
`delay.time`	The time it takes for modulation to start. Default is 0.
`ion`	Select an ion to generate an extracted ion chromatogram (EIC). If missing, the total ion chromatogram (TIC) is returned.
`mz.tol`	Whether EIC m/z range is calculated using ppm (relative) or absolute tolerance. Default is ppm
`ppm.tol`	PPM tolerance, used to calculate m/z range for EIC. Default is 20
`abs.tol`	Absolute tolerance, used to calculate m/z range for EIC. Default is 0.5 m/z
`log.scale`	Whether intensity coloring should be log scaled. Default is FALSE
`rt.min`	Minimum 1D RT to plot. Default is 0
`rt.max`	Maximum 1D RT to plot. Default is the max found in the data
`rt2.min`	Minimum 2D RT to plot. Default is 0
`rt2.max`	Maximum 2D RT to plot. Default is the modulation time
`mz.min`	Minimum m/z to plot. Default is lowest found in the data
`mz.max`	Maximum m/z to plot. Default is highest found in the data
`int.min`	Minimum intensity to plot. Default is 0
`int.max`	Maximum intensity to plot. Default is highest found in the TIC
`color.scale`	Color scale from distiller to use. Default is 'Spectral.'
`reverse.scale`	Reverse the color scale. Default is T.
`save.output`	Whether to save the output as a file. Default is FALSE
`filename`	The name for saving the file if desired. Default is '2dplot.png' plus the file selected plus the ion selected.
`filetype`	Filetype of the form ".pdf". Default is ".pdf"
`filepath`	Where to save the output file. Default is '.'
`print.output`	Whether to show the plot output. Default is TRUE
`mz.digits`	The number of digits after the decimal to show for m/z's in the plot title. Default is 4
`plot.type`	Choose from 2D ggplot, interactive 2D plotly plot ('2Di'), or an interactive 3D plotly plot ('3D'). Default is 2D