plotWfm {waveTiling} | R Documentation |
Plot function to visualize the results of the wavelet-based transcriptome analysis. Both the model fit and the significant genomic regions can be plotted and compared with the annotation.
plotWfm(fit, inf, biomartObj, minPos, maxPos, trackFeature="exon", two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)
fit |
object of class |
inf |
object of class |
biomartObj |
object of class TxDb representing an annotation database generated from BioMart. |
minPos |
minimum genomic position to plot |
maxPos |
maximum genomic position to plot |
trackFeature |
track feature. See |
two.strand |
logical indicating whether to plot two strands or not |
plotData |
logical indicating whether to plot the raw data or not |
plotMean |
logical indicating whether to plot the fitted overall mean function or not |
tracks |
vector of integers containing the track numbers to plot. Track numbers correspond with the order of the elements in the list output from the |
The plot utilities of the GenomeGraphs
-package constitute the backbone of the plotWfm
function.
nothing returned
Kristof De Beuf <kristof.debeuf@ugent.be>
[1] Durinck S, Bullard J, Spellman PT, Dudoit S: GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics 2009, 10:Article 2.
library(waveTilingData) library(TxDb.Athaliana.BioMart.plantsmart22) data(leafdevFit) data(leafdevInfCompare) trs <- transcripts(TxDb.Athaliana.BioMart.plantsmart22) sel <- trs[elementMetadata(trs)$tx_name %in% "AT1G62500.1",] start <- start(ranges(sel))-2000 end <- end(ranges(sel))+2000 plotWfm(fit=leafdevFit,inf=leafdevInfCompare,biomartObj=TxDb.Athaliana.BioMart.plantsmart22,minPos=start,maxPos=end,two.strand=TRUE,plotData=TRUE,plotMean=FALSE,tracks=c(1,2,6,10,11))