barplot ASEset objects

Description

Generates barplots for ASEset objects. Two levels of plotting detail are provided: a detailed barplot of read counts by allele useful for fewer samples and SNPs, and a less detailed barplot of the fraction of imbalance, useful for more samples and SNPs.

Usage

barplot(height, ...)

## S4 method for signature 'ASEset'
barplot(height, type = "count", sampleColour.top = NULL,
  sampleColour.bot = NULL, legend = TRUE, pValue = TRUE, strand = "*",
  testValue = NULL, testValue2 = NULL, OrgDb = NULL, TxDb = NULL,
  annotationType = c("gene", "exon", "transcript"), main = NULL,
  ylim = NULL, yaxis = TRUE, xaxis = FALSE, ylab = TRUE,
  ylab.text = NULL, xlab.text = "samples", xlab = TRUE,
  legend.colnames = "", las.ylab = 1, las.xlab = 2, cex.main = 1,
  cex.pValue = 0.7, cex.ylab = 0.7, cex.xlab = 0.7, cex.legend = 0.6,
  add = FALSE, lowerLeftCorner = c(0, 0), size = c(1, 1),
  addHorizontalLine = 0.5, add.frame = TRUE,
  filter.pValue.fraction = 0.99, legend.fill.size = 1,
  legend.interspace = 1, verbose = FALSE,
  top.fraction.criteria = "maxcount", cex.annotation = 0.7,
  ypos.annotation = 0, annotation.interspace = 1, ...)

Arguments

Details

filter.pValue.fraction is intended to remove p-value annotation with very large difference in frequency, which could just be a sequencing mistake. This is to avoid p-values like 1e-235 or similar.

sampleColourUser specified colours, either given as named colours ('red', 'blue', etc) or as hexadecimal code. Can be either length 1 for all samples, or else of a length corresponding to the number of samples for individual colouring.

Author(s)

Jesper R. Gadin, Lasse Folkersen

See Also

• The ASEset class which the barplot function can be called up on.

Examples

data(ASEset)
barplot(ASEset[1])

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/ASEset-barplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ASEset-barplot
> ### Title: barplot ASEset objects
> ### Aliases: ASEset-barplot barplot barplot,ASEset-method
> ### Keywords: barplot
> 
> ### ** Examples
> 
> 
> data(ASEset)
> barplot(ASEset[1])
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>