plotErrorBars {puma} | R Documentation

## Plot mean expression levels and error bars for one or more probesets

### 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)

[Package puma version 3.29.1 Index]