makeBoxPlot – creates boxplot of contigs included in the analysis vs those excluded

Description

makeBoxPlot – creates boxplot of contigs included in the analysis vs those excluded

Usage

## S4 method for signature 'ChrTable,LinkageGroupList'
makeBoxPlot(chrTable, linkage.contigs)

Arguments

Value

a box plot of included and excluded contigs

Examples

#make an example barplot of data

data("exampleLGList")
data("exampleChrTable")
makeBoxPlot(exampleChrTable, exampleLGList)

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)

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> library(contiBAIT)
Loading required package: BH
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/contiBAIT/makeBoxPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeBoxPlot,ChrTable,LinkageGroupList-method
> ### Title: makeBoxPlot - creates boxplot of contigs included in the
> ###   analysis vs those excluded
> ### Aliases: makeBoxPlot makeBoxPlot,ChrTable,LinkageGroupList-method
> ###   makeBoxPlot-ChrTable-LinkageGroupList-method
> 
> ### ** Examples
> 
> #make an example barplot of data
> 
> data("exampleLGList")
> data("exampleChrTable")
> makeBoxPlot(exampleChrTable, exampleLGList)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>