plotTimeCourseII: Multiplot function for RPPA time course datasets

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

Multiplot function for RPPA time course datasets

Description

plotTimeCourseII creates multiplot rectangular PDF files for time course datasets. Page layout (number of plots per page, arrangement of plots) and plot layout can be customized within the function.

Usage

    plotTimeCourseII(x,plotgroup="",filename="timeseries_multiplot.pdf",numpage=4,
	cols=2,xname="time",yname="signal",legpos="top",legrow=2,legtitle="treatment",
	legtitlepos="top",legtextsize=10,legtextcolor="black",legtitlesize=10,
	legtitlecolor="black",legtitleface="bold",legitemsize=1,plottitlesize=12,
	plottitleface="bold",xaxissize=10,yaxissize=10,xaxisface="bold",
	yaxisface="bold",xaxistextsize=8,xaxistextangle=0,yaxistextsize=8,
	linecolor="Set1")

Arguments

x	RPPA time course dataset preprocessed with the getErrorModel and averageData function
plotgroup	select the feature (eg. treatment) which should be plotted in one plot
filename	enter filename, DIR needs to be defined as your working directory, add .pdf to filename
numpage	number of plots per page
cols	number of plot columns per page
xname	title of the x axis
yname	title of the y axis
legpos	postion of the legend in context of the plot ("top","bottom","right","left"), "none" removes legend from plot
legrow	number of item rows within the legend
legtitle	title of the legend
legtitlepos	position of the legend title
legtextsize	font size of the legend text
legtextcolor	color of the legend text
legtitlesize	font size of the legend title
legtitlecolor	color of the legend title
legtitleface	font face of the legend title (eg. "bold")
legitemsize	size of the legend item pictures
plottitlesize	size of the plot title
plottitleface	font face of the plot title
xaxissize	font size of the x axis title
yaxissize	font size of the y axis title
xaxisface	font face of the x axis title
yaxisface	font face of the y axis title
xaxistextsize	font size of the x axis text
xaxistextangle	angle of the x axis text
yaxistextsize	font size of the y axis text
linecolor	color of the plot lines: either chose a scheme ("Set1","Dark2","Paired") or hand a vector of color names

Details

The plotTimeCourseII function plots RPPA timecourse datasets in multiple line charts. For each cell line and target protein a separate plot is created. The average foldchange values of different replicates and the error bars are visualized. In order to be visualized by the plotTimeCourseII function, the dataset needs to be preprocessed by the getErrorModel and averageData function from the RPPanalyzer package. Additionally the plotgroup needs to be defined if it is not named ?treatment?. The remaining arguments are optional.

Value

Generates a PDF file.

Author(s)

Johannes Bues ([e-mail])

Examples

## Not run: 

# pre-process the data
dataDir <- system.file("extdata", package="RPPanalyzer")
res <- dataPreproc(dataDir=dataDir, blocks=12, spot="aushon", exportNo=2)
# remove arrays
normdat_rm <- remove.arrays(res$normdat, param="target", arrays2rm=c("protein","blank"))
# select samples and export data
sel_sampels_A549 <- select.sample.group(normdat_rm, params=list("cell_line"="A549"), combine= FALSE)
write.Data(sel_sampels_A549, FileNameExtension="HGF_sample_data_A549")
# read selected data
dataexpression_1 <- read.table("HGF_sample_data_A549expression.txt")
# use getErrorModel function
dataexpression_2 <- getErrorModel(dataexpression_1, verbose=FALSE)
# use averageData function
dataexpression_3 <- averageData(dataexpression_2, scaling=c("slide","replicate"), 
distinguish=c("cell_line","treatment"))
# plot time course data
plotTimeCourseII(dataexpression_3, filename="timecourse_HGF_sample_data_A549.pdf", 
legpos="top", xname="time [min]",
yname="signal [a.u.]", linecolor=c("red","green","blue","black","orange","grey"))


## End(Not run)

RPPanalyzer documentation built on Aug. 28, 2023, 5:07 p.m.