plotDEXSeq {DEXSeq}R Documentation

Visualization of the fitted expression, fitted splicing or the normalized counts.

Description

The function provides a plot to visualize read count data, the fitted expression, fitted splicing and the results of the test in testForDEU. The fitted values are obtained from fitting the counts values to a certain condition from the design annotation of the glm. See fitExpToVar parameter.

Usage

plotDEXSeq(ecs, geneID, FDR=0.1, fitExpToVar="condition", 
           norCounts=FALSE, expression=TRUE, splicing=FALSE, 
           displayTranscripts=FALSE, names=FALSE, legend=FALSE, 
           color=NULL, color.samples=NULL, ...)
     

Arguments

ecs

An ExonCountSet object.

geneID

ID of the gene to visualize.

FDR

A false discovery rate used to indicate the significant exons.

fitExpToVar

A variable contained in the design annotation of the ExonCountSet, the expression values will be fitted to this variable using the formula count ~ fitExpToVar * exon using a model frame obtained from the function modelFrameForGene.

norCounts

If TRUE, provides a plot of the counts normalized by the size factors.

expression

If TRUE, the function plots the fitted EXPRESSION estimates from the glm regression.

splicing

If TRUE, the function plots the fitted SPLICING estimates from the glm regression.

displayTranscripts

If TRUE, the transcripts are displayed in the plot.

names

If TRUE, the names of the transcripts are shown.

legend

If TRUE, a legend is displayed.

color

A vector of colors for each of the levels of the factor in the design of the ExonCountSet object indicated by "fitExpToVar".

color.samples

A vector of colors for each of the samples. If NULL, the colors of each sample will be assigned according to its corresponding level from "fitExpToVar". This option is useful to visualize complex experimental designs.

...

Further graphical parameters (see par).

See Also

graphics, segments

Examples

	## Not run: 
           data("pasillaExons", package="pasilla")
	   pasillaExons <- estimateSizeFactors(pasillaExons)
	   pasillaExons <- estimateDispersions(pasillaExons)
           pasillaExons <- fitDispersionFunction( pasillaExons )
	   plotDEXSeq(pasillaExons, "FBgn0085442")
        
## End(Not run)
     

[Package DEXSeq version 1.0.2 Index]