expressionPlot: Expression Plot
In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description Usage Arguments Details Value Note Author(s) References Examples

A line plot (optionally with confidence intervals) detailing FPKM expression levels across conditions for a given gene(s) or feature(s)

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## S4 method for signature 'CuffFeature'
expressionPlot(object, logMode=FALSE, pseudocount=1.0, drawSummary=FALSE, sumFun=mean_cl_boot, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, facet = TRUE,...)

`object`	An object of class ('CuffFeature' or 'CuffGene')
`logMode`	A logical value to draw y-axis (FPKM) on log-10 scale. Default = FALSE.
`pseudocount`	A numeric value added to FPKM to avoid errors on log-10 transformation.
`drawSummary`	A logical valuie. Draws a 'summary' line with mean FPKM values for each condition.
`sumFun`	Function used to determine values for summary line. Default = mean_cl_boot
`showErrorbars`	A logical value whether or not to draw error bars.
`showStatus`	A logical value whether or not to draw visual queues for quantification status of a given gene:condition. Default = TRUE
`replicates`	A logical value whether or not to plot individual replicates or aggregate condition values.
`facet`	A logical value whether or not to facet the plot by feature id (default=TRUE).
`...`	Additional arguments

None

A ggplot2 plot object

None

Loyal A. Goff

None

	data(sampleData)
	PINK1 # sample CuffFeature object
	expressionPlot(PINK1) #Line plot of PINK1 FPKM values
	expressionPlot(PINK1@isoforms) #Line plot of PINK1 FPKM values faceted by isoforms