MALDIquant: plotMsiSlice-methods – R documentation

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plotMsiSlice-methods

Plots a Mass Spectrometry Imaging dataset.

Description

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.

Usage

## 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

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"))))

MALDIquant

Quantitative Analysis of Mass Spectrometry Data

v1.19.3

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)

Initial release

2019-05-12