Plot ordering of contigs within a single linkage group.

Description

Plot ordering of contigs within a single linkage group.

Usage

plotContigOrder(contigOrder, lg)

Arguments

Value

A ggplot object (which will be plotted automatically if not assigned).

Examples

#Get a data.frame of ordered contigs from cells from the same organism, aligned to the same genome
 
data("exampleLGList")
data("exampleWCMatrix")
data("exampleStrandFreq")
data("exampleReadCounts")
contigOrder <- orderAllLinkageGroups(exampleLGList, 
								     exampleWCMatrix, 
								     exampleStrandFreq, 
								     exampleReadCounts)
plotContigOrder(contigOrder)

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/plotContigOrder.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotContigOrder
> ### Title: Plot ordering of contigs within a single linkage group.
> ### Aliases: plotContigOrder
> 
> ### ** Examples
> 
> #Get a data.frame of ordered contigs from cells from the same organism, aligned to the same genome
>  
> data("exampleLGList")
> data("exampleWCMatrix")
> data("exampleStrandFreq")
> data("exampleReadCounts")
> contigOrder <- orderAllLinkageGroups(exampleLGList, 
+ 								     exampleWCMatrix, 
+ 								     exampleStrandFreq, 
+ 								     exampleReadCounts)
-> Ordering fragments in LG1
     -> Found better ordering!
-> Ordering fragments in LG2
     -> Found better ordering!
-> Ordering fragments in LG3
     -> Found better ordering!
-> Ordering fragments in LG4
     -> Found better ordering!
     -> Found better ordering!
     -> Found better ordering!
> plotContigOrder(contigOrder)
Warning message:
In grep(paste(unique(masterGroups)[lg], "\.", sep = ""), contigOrder[,  :
  argument 'pattern' has length > 1 and only the first element will be used
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>