plotRaw: Plot method for 'ptrRaw' objects

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

Plot method for 'ptrRaw' objects

Description

Displays the image of the matrix of intensities, the TIC and the TIS, for the selected m/z and time ranges

Usage

plotRaw(
  object,
  mzRange,
  timeRange = c(NA, NA),
  type = c("classical", "plotly")[1],
  ppm = 2000,
  palette = c("heat", "revHeat", "grey", "revGrey", "ramp")[1],
  showVocDB = TRUE,
  figure.pdf = "interactive",
  ...
)

## S4 method for signature 'ptrRaw'
plotRaw(
  object,
  mzRange,
  timeRange = c(NA, NA),
  type = c("classical", "plotly")[1],
  ppm = 2000,
  palette = c("heat", "revHeat", "grey", "revGrey", "ramp")[1],
  showVocDB = TRUE,
  figure.pdf = "interactive",
  ...
)

## S4 method for signature 'ptrSet'
plotRaw(
  object,
  mzRange,
  timeRange = c(NA, NA),
  type = c("classical", "plotly")[1],
  ppm = 2000,
  palette = c("heat", "revHeat", "grey", "revGrey", "ramp")[1],
  showVocDB = TRUE,
  figure.pdf = "interactive",
  fileNames = NULL,
  ...
)

Arguments

object	An S4 object of class ptrRaw-class or ptrSet
mzRange	Either a vector of 2 numerics indicating the m/z limits or an integer giving a nominal m/z
timeRange	Vector of 2 numerics giving the time limits
type	Character: plot type; either 'classical' [default] or 'plotly'
ppm	Integer: Half size of the m/z window when mzRange is set to a nominal mass
palette	Character: Color palette for the 'classical' plot; either 'heat' [default], 'revHeat', 'grey', 'revGrey' or 'ramp'
showVocDB	Logical: Should putative m/z annotations from the internal package database be displayed (default is TRUE)
figure.pdf	Character: Either 'interactive' [default], or the filename of the figure to be saved (with the 'pdf' extension); only available for the 'classical' display
...	not used
fileNames	vector of character. The file names of the ptrSer that you want to plot. Could be in basename or fullname.

Value

Invisibly returns a list of the raw (sub)matrix 'rawsubM' and the voc (sub)database 'vocsubDB'

Examples

dirRaw <- system.file("extdata/exhaledAir", package = "ptairData")
exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset", 
mzCalibRef = c(21.022, 60.0525), fracMaxTIC = 0.7, saveDir = NULL )
ptairMS::plotRaw(exhaledPtrset ,mzRange=59,fileNames='ind1-1.h5')

patientRaw <- ptairMS::readRaw(system.file('extdata/exhaledAir/ind1/ind1-1.h5',  
package = 'ptairData'),  mzCalibRef=c(21.022,59.049,75.05))
ptairMS::plotRaw(patientRaw, mzRange = 59)
ptairMS::plotRaw(patientRaw, mzRange = 59, type = 'plotly')

camilleroquencourt/ptairMS documentation built on April 24, 2024, 9:03 p.m.