expressionBarplot: Barplot

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

Description

A barplot of FPKM values with confidence intervals for a given gene, set of genes, or features of a gene (e.g. isoforms, TSS, CDS, etc).

Usage

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## S4 method for signature 'CuffFeatureSet'
expressionBarplot(object, logMode=TRUE, pseudocount=1.0, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, ...)

Arguments

object

An object of class ('CuffFeatureSet','CuffGeneSet','CuffFeature','CuffGene')

logMode

A logical value whether or not to draw y-axis on log10 scale. Default = FALSE.

pseudocount

Numerical value added to each FPKM during log-transformation to avoid errors.

showErrorbars

A logical value whether or not to draw error bars. Default = TRUE

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.

...

Additional arguments.

Details

None

Value

A ggplot2 plot object

Note

Need to implement logMode and features for this plotting method.

Author(s)

Loyal A. Goff

References

None

Examples

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	data(sampleData)
	PINK1 # sample CuffFeature object
	expressionBarplot(PINK1) #Barplot of PINK1 FPKM values
	expressionBarplot(PINK1@isoforms) #Barplot of PINK1 FPKM values faceted by isoforms

cummeRbund documentation built on May 2, 2018, 3:12 a.m.