lattice barplot inner functions for ASEset objects

Description

Generates lattice 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

barplotLatticeFraction(identifier, ...)

barplotLatticeCounts(identifier, ...)

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

a <- ASEset
name <- rownames(a)[1]

barplotLatticeFraction(identifier=name, x=a, astrand="+") 
barplotLatticeCounts(identifier=name,  x=a, astrand="+") 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> 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/barplot-lattice-support.Rd_%03d_medium.png", width=480, height=480)
> ### Name: barplot-lattice-support
> ### Title: lattice barplot inner functions for ASEset objects
> ### Aliases: barplot-lattice-support barplotLatticeCounts
> ###   barplotLatticeFraction
> ### Keywords: barplot
> 
> ### ** Examples
> 
> 
> a <- ASEset
> name <- rownames(a)[1]
> 
> barplotLatticeFraction(identifier=name, x=a, astrand="+") 
> barplotLatticeCounts(identifier=name,  x=a, astrand="+") 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>