plotDist: Plots the distribution of features across fractions

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Plots the distribution of features across fractions

Description

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(s)

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")

lgatto/pRoloc documentation built on Nov. 27, 2024, 12:14 a.m.