plotDist {pRoloc} | R Documentation

## 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")

[Package pRoloc version 1.34.0 Index]