waveTiling (version 1.14.0)

plotWfm: plot model fit and genomic regions

Description

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.

Usage

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

Arguments

fit

object of class WfmFit

inf

object of class WfmInf

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 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.

Value

Details

The plot utilities of the GenomeGraphs-package constitute the backbone of the plotWfm function.

References

[1] Durinck S, Bullard J, Spellman PT, Dudoit S: GenomeGraphs: integrated genomic data visualization with R. BMC Bioinformatics 2009, 10:Article 2.

Examples

  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))