peakPantheR_plotPeakwidth: Plot peak value and peakwidth by acquisition time or in input...

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Plot peak value and peakwidth by acquisition time or in input order

Description

For a single ROI, plot the peak value and peakwidth (RT, m/z, ...) of detected peaks across multiple samples, by acquisition time or in input order. If rotateAxis=FALSE x is run order / plot order, y is the apexValue / widthMin / widthMax, if rotateAxis=TRUE x is the measurement values and y the run order.

Usage

peakPantheR_plotPeakwidth(
    apexValue,
    widthMin = NULL,
    widthMax = NULL,
    acquTime = NULL,
    varName = "variable",
    sampleColour = NULL,
    rotateAxis = FALSE,
    verbose = TRUE
)

Arguments

apexValue	(float) vector of apex value
widthMin	(float) vector of detected peak minimum peakwidth value or NULL (if NULL no peakwidth)
widthMax	(float) vector of detected peak maximum peakwidth value or NULL (uf NULL no peakwidth)
acquTime	(POSIXct) vector of sample acquisition time as POSIXct or NULL (if NULL points are plotted in the order values are passed as input with the first on top or left)
varName	(str) Name of the variable to plot
sampleColour	(str) NULL or vector colour for each sample (same length as apexValue, widthMin, widthMax, acquTime)
rotateAxis	(bool) if TRUE x and y axis are reversed
verbose	(bool) if TRUE message when NA scans are removed

Value

Grob (ggplot object)

Examples

## Input data
apexVal <- c(1, 2, 3, 4)
minVal  <- c(0, 0, 2, 2)
maxVal  <- c(2, 4, 4, 5)
acqTime <- as.POSIXct(c('2017-07-13 21:06:14', '2017-07-14 21:06:14', 
                        '2017-07-15 21:06:14', '2017-07-16 21:06:14'))

## Plot 4 sampels with colour
peakPantheR_plotPeakwidth(apexValue=apexVal, widthMin=minVal,widthMax=maxVal,
                        acquTime=NULL, varName='Test variable 1',
                        sampleColour=c('blue','red','green','orange'),
                        rotateAxis=FALSE, verbose=FALSE)

## Plot 4 samples with colour by acquisition time
peakPantheR_plotPeakwidth(apexValue=apexVal, widthMin=minVal,widthMax=maxVal,
                        acquTime=acqTime, varName='Test variable 2',
                        sampleColour=c('blue','red','green','orange'),
                        rotateAxis=FALSE, verbose=FALSE)

## Plot 4 samples with colour, rotate axis
peakPantheR_plotPeakwidth(apexValue=apexVal, widthMin=minVal,widthMax=maxVal,
                        acquTime=NULL, varName='Test variable 3',
                        sampleColour=c('blue','red','green','orange'),
                        rotateAxis=TRUE, verbose=FALSE)

## Plot 4 samples with colour by acquisition time, rotate axis
peakPantheR_plotPeakwidth(apexValue=apexVal, widthMin=minVal,widthMax=maxVal,
                        acquTime=acqTime, varName='Test variable 4',
                        sampleColour=c('blue','red','green','orange'),
                        rotateAxis=FALSE, verbose=FALSE)

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.