plotFeatures: Plot raw average spectrum around a mzRange

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

Plot raw average spectrum around a mzRange

Description

Plot the raw data spectrum for several files in a ptrSet object around the mz masses. The expiration average spectrum is in full lines, and background in dashed lines.

Usage

plotFeatures(
  set,
  mz,
  typePlot = "plotly",
  addFeatureLine = TRUE,
  ppm = 2000,
  pdfFile = NULL,
  fileNames = NULL,
  colorBy = "rownames"
)

## S4 method for signature 'ptrSet'
plotFeatures(
  set,
  mz,
  typePlot = "plotly",
  addFeatureLine = TRUE,
  ppm = 2000,
  pdfFile = NULL,
  fileNames = NULL,
  colorBy = "rownames"
)

Arguments

set	a ptrSet-class object
mz	the mz values to plot
typePlot	set "plotly" to get an interactive plot, or "ggplot"
addFeatureLine	boolean. If TRUE a vertical line at the mz masses is plotted
ppm	windows size of the plot round mz in ppm
pdfFile	a file path to save a pdf with a individual plot per file
fileNames	vector of character. The file names you want to plot. If NULL, it plot all files
colorBy	character. A column name of sample metadata by which the line are colored.

Value

a plotly or ggplot2 object

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 )
plotF<-plotFeatures(exhaledPtrset ,mz=59.049,type="ggplot",colorBy="subfolder")
print(plotF)

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