plotDEXSeq {DEXSeq} | R Documentation |
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.
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, ...)
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 |
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 |
graphics, segments
## Not run: data("pasillaExons", package="pasilla") pasillaExons <- estimateSizeFactors(pasillaExons) pasillaExons <- estimateDispersions(pasillaExons) pasillaExons <- fitDispersionFunction( pasillaExons ) plotDEXSeq(pasillaExons, "FBgn0085442") ## End(Not run)