plotTimeCourse: Draw time course from RPPA data

In RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Draw time course from RPPA data

Description

Draws time course data from a RPPA data list and calculates a mathematical model on the time course data.

Usage

plotTimeCourse(x, tc.identifier = 
			c("sample", "stimulation", "inhibition", "stim_concentration"),
		tc.reference=NULL, plot.split = "experiment", file = NULL,
		arrays2rm = c("protein", "Blank"), plotformat = "stderr",
		log=TRUE, color=NULL, xlim = NULL, ylim = NULL)

Arguments

x	List containing RPPA data set
tc.identifier	character string describing the column names in the sampledescription that identifies the individual time course experiments
tc.reference	character string describing the sample that will be used as reference for the time course plots.
plot.split	character string describing the column names in sampledescription that defines the argument that devides between different plots
file	character string for the name of the exported file
arrays2rm	character strings identifying the targets that should be from the time course plots
plotformat	character string defining the plot type: rawdata for plotting the connected medians plus standard deviation of the data, spline and both for plotting the a spline fit through the data or both raw data and spline, as well as a confidence band showing the standard error of the spline fit; spline_noconf only plots the spline without confidence band. errbar will show the spline fit plus raw data without connecting the medians by a line, stderr will show a less crowded version of the spline plus standard error represented as simple error bars (which is the default).
log	logical, if true time courses signal intensities will be plotted at log2 scale
color	Vector holding the colors for the samples to be plot. If NULL, colors will be generated.
xlim	Limits for x-axis. If NULL (default) limits are generated for each timeseries plot. If a range (numeric vector of length 2) is given, this is used for all plots.
ylim	Analogous to xlim for y-axis limits.

Details

This function plots RPPA time course experiments from data sets with aggregated replicate spots. A column time containing numeric values is required in the sampledescription file. One or several column in the sampledescription file should be able to indentify the individual experiments described in argument tc.identifier. One column should provide a parameter plot.split to split the whole data set into different comparable time courses that have to be plotted together.

Different plotting options can be specified with the argument plotformat. Option both is most informative, since it shows the original data plus standard deviations at each time point, combined with a spline fit and the standard error of the fit.

Value

generates a PDF file

Author(s)

Heiko Mannsperger <[e-mail]

Examples

## Not run: 
	library(RPPanalyzer)
	data(dataII)
	plotTimeCourse(dataII,
		tc.identifier=c("sample","stimulation","stim_concentration","inhibition")
        ,plot.split="experiment",plotformat="stderr")
    plotTimeCourse(dataII,
		tc.identifier=c("sample","stimulation","stim_concentration","inhibition")
        ,plot.split="experiment",plotformat="errbar")
    plotTimeCourse(dataII,
		tc.identifier=c("sample","stimulation","stim_concentration","inhibition")
        ,plot.split="experiment",plotformat="both")
    plotTimeCourse(dataII,
		tc.identifier=c("sample","stimulation","stim_concentration","inhibition")
        ,plot.split="experiment",plotformat="rawdata")
    plotTimeCourse(dataII,
		tc.identifier=c("sample","stimulation","stim_concentration","inhibition")
        ,plot.split="experiment",plotformat="spline")
    plotTimeCourse(dataII,
		tc.identifier=c("sample","stimulation","stim_concentration","inhibition")
        ,plot.split="experiment",plotformat="spline_noconf")
               

## End(Not run)

RPPanalyzer documentation built on May 29, 2024, 5:43 a.m.