plotErrorBars: Plot mean expression levels and error bars for one or more...

In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description

This produces plots of probesets of interest.

Usage

plotErrorBars(
	eset
,	probesets = if(dim(exprs(eset))[1] <= 12) 1:dim(exprs(eset))[1] else 1
,	arrays = 1:dim(pData(eset))[1] # default is to use all
,	xlab = paste(colnames(pData(eset))[1:numOfFactorsToUse(eset)], collapse=":")
,	ylab = "Expression Estimate"
,	xLabels = apply(
                  as.matrix(pData(eset)[arrays,1:numOfFactorsToUse(eset)])
                , 1
                , function(mat){paste(mat, collapse=":")}
                )
,	ylim = NA
,	numOfSEs = qnorm(0.975)
,	globalYlim = FALSE # Not yet implemented!
,	plot_cols = NA
,	plot_rows = NA
,	featureNames = NA
,	showGeneNames = FALSE
,	showErrorBars = if(
					length(assayDataElement(eset,"se.exprs"))==0 ||
					length(assayDataElement(eset,"se.exprs")) == sum(is.na(assayDataElement(eset,"se.exprs")))
					) FALSE else TRUE
,	plotColours = FALSE
,	log.it = if(max(exprs(eset)) > 32) TRUE else FALSE
,	eset_comb = NULL
,	jitterWidth = NA
,	qtpcrData = NULL
, ...
)

Arguments

eset	An object of class ExpressionSet. This is the main object being plotted.
probesets	A vector of integers indicating the probesets to be plotted. These integers refer to the row numbers of the eset.
arrays	A vector of integers indicating the arrays to be shown on plots.
xlab	Character string of title to appear on x-axis
ylab	Character string of title to appear on y-axis
xLabels	Vector of strings for labels of individual points on x-axis.
ylim	2-element numeric vector showing minimum and maximum values for y-axis.
numOfSEs	Numeric indicating the scaling for the error bars. The default value give error bars that include 95% of expected values.
globalYlim	Not yet implemented!
plot_cols	Integer specifying number of columns for multi-figure plot.
plot_rows	Integer specifying number of rows for multi-figure plot.
featureNames	A vector of strings for featureNames (Affy IDs). This is an alternative (to the probesets argument) way of specifying probe sets.
showGeneNames	Boolean indicating whether to use Affy IDs as titles for each plot.
showErrorBars	Boolean indicating whether error bars should be shown on plots.
plotColours	A vector of colours to plot.
log.it	Boolean indicating whether expression values should be logged.
eset_comb	An object of class ExpressionSet. This is a secondary object to be plotted on the same charts as eset. This should be an object created using pumaComb and pumaCombImproved which holds the values created by combining information from the replicates of each condition.
jitterWidth	Numeric indicating the x-axis distance between replicates of the same condition.
qtpcrData	A 2-column matrix of qRT-PCR values (or other data to be plotted on the same charts).
...	Additional arguments to be passed to plot.

Value

This function has no return value. The output is the plot created.

Author(s)

Richard D. Pearson

Examples

	#	Next 4 lines commented out to save time in package checks, and saved version used
    # if (require(affydata)) {
	#	data(Dilution)
	#	eset_mmgmos <- mmgmos(Dilution)
	# }
	data(eset_mmgmos)
	plotErrorBars(eset_mmgmos)
	plotErrorBars(eset_mmgmos,1:6)

puma documentation built on Nov. 8, 2020, 11:08 p.m.