plotRaw {ptairMS} | R Documentation |
Displays the image of the matrix of intensities, the TIC and the TIS, for the selected m/z and time ranges
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, ... )
object |
An S4 object of class |
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. |
Invisibly returns a list of the raw (sub)matrix 'rawsubM' and the voc (sub)database 'vocsubDB'
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')