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Last data update: 2014.03.03

R: locationplot ASEset objects

ASEset-locationplot

R Documentation

locationplot ASEset objects

Description

plotting ASE effects over a specific genomic region

Usage

locationplot(x, ...)

## S4 method for signature 'ASEset'
locationplot(x, type = "fraction", strand = "*",
  yaxis = TRUE, xaxis = FALSE, xlab = FALSE, ylab = TRUE,
  xlab.text = "", ylab.text = "", legend.colnames = "", size = c(0.8,
  1), main = NULL, pValue = FALSE, cex.main = 0.7, cex.ylab = 0.6,
  cex.legend = 0.5, OrgDb = NULL, TxDb = NULL, verbose = TRUE,
  top.fraction.criteria = "maxcount", allow.whole.chromosome = FALSE, ...)

Arguments

`x`	an ASEset object.
`...`	arguments passed on to barplot function
`type`	'fraction' or 'count'
`strand`	'+','-','*' or 'both'. This argument determines which strand is plotted. See `getAlleleCounts` for more information on strand.
`yaxis`	wheter the y-axis is to be displayed or not
`xaxis`	wheter the x-axis is to be displayed or not
`xlab`	showing labels for the tic marks
`ylab`	showing labels for the tic marks
`xlab.text`	xlab text
`ylab.text`	ylab text
`legend.colnames`	gives colnames to the legend matrix
`size`	will give extra space in the margins of the inner plots
`main`	text to use as main label
`pValue`	Display p-value
`cex.main`	set main label size
`cex.ylab`	set ylab label size
`cex.legend`	set legend label size
`OrgDb`	an OrgDb object from which to plot a gene map. If given together with argument TxDb this will only be used to extract genesymbols.
`TxDb`	a TxDb object from which to plot an exon map.
`verbose`	Setting `verbose=TRUE` gives details of procedure during function run
`top.fraction.criteria`	'maxcount', 'ref' or 'phase'
`allow.whole.chromosome`	logical, overrides 200kb region limit, defaults to FALSE

Details

The locationplot methods visualises how fractions are distributed over a larger region of genes on one chromosome. It takes and ASEset object as well as additional information on plot type (see barplot), strand type (see getAlleleCounts), colouring, as well as annotation. The annotation is taken either from the bioconductor OrgDb-sets, the TxDb sets or both. It is obviously important to make sure that the genome build used is the same as used in aligning the RNA-seq data.

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples



data(ASEset)
locationplot(ASEset)

#SNPs are plotted in the order in which they are found. 
#This can be sorted according to location as follows:
locationplot(ASEset[order(start(rowRanges(ASEset))),])

#for ASEsets with fewer SNPs the 'count' type plot is
# useful for detailed visualization.
locationplot(ASEset,type='count',strand='*')

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(AllelicImbalance)
Loading required package: grid
Loading required package: GenomicRanges
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: 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: GenomeInfoDb
Loading required package: SummarizedExperiment
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: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AllelicImbalance/locationplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ASEset-locationplot
> ### Title: locationplot ASEset objects
> ### Aliases: ASEset-locationplot locationplot locationplot,ASEset-method
> ### Keywords: locationplot
> 
> ### ** Examples
> 
> 
> 
> data(ASEset)
> locationplot(ASEset)
> 
> #SNPs are plotted in the order in which they are found. 
> #This can be sorted according to location as follows:
> locationplot(ASEset[order(start(rowRanges(ASEset))),])
> 
> #for ASEsets with fewer SNPs the 'count' type plot is
> # useful for detailed visualization.
> locationplot(ASEset,type='count',strand='*')
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>