plotRaw {ptairMS} | R 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')

[Package ptairMS version 1.2.0 Index]