R Graphical Manual

Browse All

Last data update: 2014.03.03

R: plot model fit and genomic regions

plotWfm

R Documentation

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.

Details

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

Value

nothing returned

Author(s)

Kristof De Beuf <kristof.debeuf@ugent.be>

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))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(waveTiling)
Loading required package: oligo
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: GenomeGraphs
Loading required package: biomaRt
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/waveTiling/plotWfm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotWfm
> ### Title: plot model fit and genomic regions
> ### Aliases: plotWfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   library(waveTilingData)
>   library(TxDb.Athaliana.BioMart.plantsmart22)
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
>   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))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>