MALDIquant (version 1.11)

plotImsSlice: Plots an Imaging Mass Spectrometry dataset.

Description

This function allows to plot a slice of an Imaging Mass Spectrometry dataset represented by a list of AbstractMassObject objects.

Usage

plotImsSlice(x, range=c(0, Inf),
             sub=paste0("m/z: ", range[1L], "-", range[2L], ""),
             removeEmptyRows=TRUE, removeEmptyCols=TRUE,
             colRamp=colorRamp(c("black", "blue", "green", "yellow", "red")),
             interpolate=FALSE, ...)

Arguments

x

list, list of MassSpectrum/MassPeaks objects.

range

double, length 2, range/thickness of the slice.

sub

character, sub title for the plot, see title.

removeEmptyRows

logical, Should empty rows be removed?

removeEmptyCols

logical, Should empty columns be removed?

colRamp

colours as colorRamp function, see colorRamp for details.

interpolate

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

...

arguments to be passed to plot.

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

See Also

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

Website: http://strimmerlab.org/software/maldiquant/

Example: https://github.com/sgibb/MALDIquantExamples/blob/master/vignettes/ims.Rnw

Shiny example: http://spark.rstudio.com/sgibb/ims/, https://github.com/sgibb/ims-shiny/

Examples

plotImsSlice(spectra, range = c(3361.8, 3362.8))