Plots the distribution of features across fractions

Produces a line plot showing the feature abundances across the fractions.

Usage

plotDist(
  object,
  markers,
  fcol = NULL,
  mcol = "steelblue",
  pcol = getUnknowncol(),
  alpha = 0.3,
  type = "b",
  lty = 1,
  fractions = sampleNames(object),
  ylab = "Intensity",
  xlab = "Fractions",
  ylim,
  ...
)

Arguments

object: An instance of class MSnSet.
markers: A character, numeric or logical of appropriate length and or content used to subset object and define the organelle markers.
fcol: Feature meta-data label (fData column name) defining the groups to be differentiated using different colours. If NULL (default) ignored and mcol and pcol are used.
mcol: A character define the colour of the marker features. Default is "steelblue".
pcol: A character define the colour of the non-markers features. Default is the colour used for features of unknown localisation, as returned by getUnknowncol.
alpha: A numeric defining the alpha channel (transparency) of the points, where 0 <= alpha <= 1, 0 and 1 being completely transparent and opaque.
type: Character string defining the type of lines. For example "p" for points, "l" for lines, "b" for both. See plot for all possible types.
lty: Vector of line types for the marker profiles. Default is 1 (solid). See par for details.
fractions: A character defining the phenoData variable to be used to label the fraction along the x axis. Default is to use sampleNames(object).
ylab: y-axis label. Default is "Intensity".
xlab: x-axis label. Default is "Fractions".
ylim: A numeric vector of length 2, giving the y coordinates range.
...: Additional parameters passed to plot.

Value

Used for its side effect of producing a feature distribution plot. Invisibly returns the data matrix.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(tan2009r1)
j <- which(fData(tan2009r1)$markers == "mitochondrion")
i <- which(fData(tan2009r1)$PLSDA == "mitochondrion")
plotDist(tan2009r1[i, ], markers = featureNames(tan2009r1)[j])

plotDist(tan2009r1[i, ], markers = featureNames(tan2009r1)[j],
         fractions = "Fractions")

## plot and colour all marker profiles
tanmrk <- markerMSnSet(tan2009r1)
plotDist(tanmrk, fcol = "markers")