expressionPlot: Expression Plot

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description

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

Usage

## 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

	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

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.