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
).