Visualization of the per gene DEXSeq results.

The function provides a plot to visualize read count data, expression and exon usage coefficients estimated from fitting a GLM model 'counts ~ fitExpToVar * exon'. The model frame used can be found in object@modelFrameBM. One GLM is fitted for each gene.

Usage

plotDEXSeq(object, geneID, FDR=0.1, fitExpToVar="condition", 
    norCounts=FALSE, expression=TRUE, splicing=FALSE, 
    displayTranscripts=FALSE, names=FALSE, legend=FALSE, 
    color=NULL, color.samples=NULL, transcriptDb=NULL,
    additionalAnnotation=NULL, maxRowsMF=2400, ...)

Arguments

object

A DEXSeqResults object. A DEXSeqDataSet object is also accepted, but only with the possibility of plotting the normalized read counts for each exon bin.

geneID

Gene identifier to visualize.

FDR

A false discovery rate.

fitExpToVar

A variable contained in the sample annotation of the DEXSeqDataSet, the expression values will be fitted to this variable using the formula count ~ fitExpToVar * exon.

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 samples gene expression effects are averaged out, leaving only exon usage coefficients.

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.

transcriptDb

A TxDb object, as defined in the GenomicFeatures package. This parameter is optional. If present and if 'displayTranscripts=TRUE', the transcript UTRs will be distinguished from the coding regions.

additionalAnnotation

A GRangesList object specifying the genomic coordinates of annotation features that should be plotted. This parameter is useful, for example, when one wants to show protein domain annotations.

maxRowsMF

See ?estimateExonFoldChanges for details.

...

Further graphical parameters (see par).

See also

graphics, segments

Examples

if (FALSE) { # \dontrun{
  data(pasillaDEXSeqDataSet, package="pasilla")
  dxd <- estimateSizeFactors( dxd )
  dxd <- estimateDispersions( dxd )
  dxd <- testForDEU( dxd )
  dxr <- DEXSeqResults( dxd )

  plotDEXSeq( dxr, "FBgn0010909" )
} # }