plotRaw: Plot method for 'ptrRaw' objects

plotRawR Documentation

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 June 9, 2024, 10:35 a.m.