plotWfm: plot model fit and genomic regions
In waveTiling: Wavelet-Based Models for Tiling Array Transcriptome Analysis

Description Usage Arguments Details Value Author(s) References Examples

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.

1	plotWfm(fit, inf, biomartObj, minPos, maxPos, trackFeature="exon", two.strand=TRUE, plotData=TRUE, plotMean=TRUE, tracks=0)

`fit`	object of class `WfmFit`
`inf`	object of class `WfmInf`
`biomartObj`	object of class TranscriptDb representing an annotation database generated from BioMart.
`minPos`	minimum genomic position to plot
`maxPos`	maximum genomic position to plot
`trackFeature`	track feature. See `GenomeGraphs`-package. Default is `exon`.
`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 `getGenmicRegions`-function.

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.plantsmart12)
  data(leafdevFit)
  data(leafdevInfCompare)
  trs <- transcripts(TxDb.Athaliana.BioMart.plantsmart12)
  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.plantsmart12,minPos=start,maxPos=end,two.strand=TRUE,plotData=TRUE,plotMean=FALSE,tracks=c(1,2,6,10,11))