expressionPlot: Expression Plot

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

View source: R/methods-CuffFeature.R View source: R/methods-CuffFeatureSet.R

Description

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

Usage

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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,...)

Arguments

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

Details

None

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

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	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

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