plotMsiSlice-methods function

Plots a Mass Spectrometry Imaging dataset.

This function allows to plot a slice of a mass spectrometry imaging dataset represented by a list of AbstractMassObject objects or an array or a matrix. methods

## S4 method for signature 'list'
plotMsiSlice(x, center, tolerance,
  colRamp=colorRamp(c("black", "blue", "green", "yellow", "red")),
  interpolate=FALSE, legend=TRUE, alignLabels=FALSE, combine=FALSE,
  ...)
## S4 method for signature 'array'
plotMsiSlice(x,
  colRamp=colorRamp(c("black", "blue", "green", "yellow", "red")),
  interpolate=FALSE, legend=TRUE, alignLabels=FALSE, combine=FALSE,
  plotInteractive=FALSE, ...)
## S4 method for signature 'matrix'
plotMsiSlice(x,
  colRamp=colorRamp(c("black", "blue", "green", "yellow", "red")),
  interpolate=FALSE, scale=TRUE, legend=scale, ...)

Arguments

• x: The mass spectrometry imaging dataset. It could be a list of MassSpectrum/MassPeaks objects or an array (e.g. generated by msiSlices) or a matrix.

• center: double, if x is a list of MassSpectrum/MassPeaks objects this argument represent the center mass value of the slices, see msiSlices for details.

• tolerance: double, if center is given tolerance

  specifies the thickness of the slices (center + c(-tolerance, tolerance)), see msiSlices for details.

• colRamp: colours as colorRamp function, see colorRamp for details. If combine=TRUE

  multiple colour functions must be applied as list with an length that equals the number of given centers.

• interpolate: logical, use linear interpolation when drawing the image, see rasterImage for details.

• scale: logical, if TRUE all values are divided by the maximal value of the slice to get values between 0 and 1.

• legend: logical, if TRUE a reference color gradient is plotted on the right hand side of the plot. The upper color represents the highest value in the slice and the lower color the lowest value respectively. The legend is disabled if scale=FALSE.

• alignLabels: logical, if combine=TRUE and alignLabels=TRUE the center positions below the legend are aligned on the right margin otherwise the aligned to their corresponding gradient.

• combine: logical, if TRUE multiple centers are plotted in one image. Therefore it would be necessary to apply a list of colRamp

  functions (one function for each center). The intensity values for each center of each pixel are compared against each other and the highest scaled intensity determines the center (and the corresponding colRamp).

• plotInteractive: logical, if the slice array contains multiple centers, combine=FALSE and an interactive plotting device is used a warning is thrown and only the first center would be plotted. Use plotInteractive=TRUE to overwrite this behaviour and to plot multiple centers on an interactive device.

• ...: arguments to be passed to plot, e.g. main.

Details

Each MassSpectrum/MassPeaks object in x must contain a list named imaging with an element pos that stores the x and y value of the spectrum, e.g.:

> metaData(spectra[[1]])$imaging$pos
x y
1 5

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

AbstractMassObject, MassSpectrum, MassPeaks, coordinates,AbstractMassObject-method, msiSlices, plot,MassSpectrum,missing-method

Please find real examples on:

Website: https://strimmerlab.github.io/software/maldiquant/

Vignette: https://github.com/sgibb/MALDIquantExamples/raw/master/inst/doc/nyakas2013.pdf

Shiny: https://github.com/sgibb/ims-shiny/

Examples

## load package
library("MALDIquant")

## load example data
data("fiedler2009subset", package="MALDIquant")

## please note: this is NOT a MSI data set
## we just add some coordinates for demonstration
coordinates(fiedler2009subset) <- cbind(x=rep(1:4, 2), y=rep(1:2, each=4))

plotMsiSlice(fiedler2009subset, center=8936.97, tolerance=0.25)

plotMsiSlice(fiedler2009subset, center=c(5864.49, 8936.97), tolerance=0.25,
             combine=TRUE,
             colRamp=list(colorRamp(c("#000000", "#FF00FF")),
                          colorRamp(c("#000000", "#00FF00"))))