pRoloc (version 1.12.4)

plotDist: Plots the distribution of features across fractions

Description

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

Usage

plotDist(object, markers, mcol = "steelblue", pcol = "grey90", alpha = 0.3, type = "b", lty = 1, 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.

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 "grey90".

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

An optional character defining the phenoData variable to be used to label the fraction along the x axis. If missing, the phenoData variables are searched for a match to fraction. If no match is found, the fractions are labelled as numericals.

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.

Examples

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