plotTIC: plot the Total Ion sptectrum (TIC) for one or several files.

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

plot the Total Ion sptectrum (TIC) for one or several files.

Description

plot the Total Ion sptectrum (TIC) for one or several files.

Usage

plotTIC(
  object,
  type = c("plotly", "ggplot")[1],
  baselineRm = FALSE,
  showLimits = FALSE,
  ...
)

## S4 method for signature 'ptrRaw'
plotTIC(object, type, baselineRm, showLimits, fracMaxTIC = 0.8, ...)

## S4 method for signature 'ptrSet'
plotTIC(
  object,
  type,
  baselineRm,
  showLimits,
  pdfFile = NULL,
  fileNames = NULL,
  colorBy = "rownames",
  normalizePrimariIon = FALSE,
  ...
)

Arguments

object	ptrSet or ptrRaw S4 object
type	set 'plotly' to get an interactive plot, and 'ggplot' for classical plot.
baselineRm	logical. If TRUE, remove the baseline of the TIC
showLimits	logical. If TRUE, add the time limits to the plot (obtain with the 'fracMaxTIC' argument or 'createPtrSet' function)
...	not used
fracMaxTIC	Percentage (between 0 and 1) of the maximum of the Total Ion Current (TIC) amplitude with baseline removal. We will analyze only the part of the spectrum where the TIC intensity is higher than 'fracMaxTIC * max(TIC) '. If you want to analyze the entire spectrum, set this parameter to 0.
pdfFile	a absolute file path. A pdf will be generated with a plot for each file, caints TIC and time limits.
fileNames	vector of character. The file names of the ptrSer that you want to plot. Could be in basename or fullname.
colorBy	character. A name of the ptrSet's sampleMetaData column, to display with the same color files of same attributes.
normalizePrimariIon	should the TIC be normalized by the primary ion

Value

a plotly of ggplot2 object.

Examples

### ptrRaw object

library(ptairData)
filePath <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', 
package = 'ptairData')
raw <- readRaw(filePath)
p <- plotTIC(raw)
p
dirRaw <- system.file("extdata/exhaledAir", package = "ptairData")
exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset", 
mzCalibRef = c(21.022, 60.0525), fracMaxTIC = 0.7, saveDir = NULL )
plotTIC(exhaledPtrset ,type='ggplot')

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