Display the chromosome distribution of structural variations

Description

Display the chromosome distribution of structural variations by splitting the chromosomes into windows of specific size and counting the number of structural variations in each window.

Usage

    plotChromosome(genomeAnnotation, structuralVariation, windowSize=1000000)

Arguments

Details

To visualize the distribution of structural variations in the whole genome, chromosomes were splitted into windows of specific size (default 1 Mb) and the number of structural variations in each window were counted. The number of structural variations were shown using circular barplot.

Value

A circular plot with five layers:

• the circular view of genome ideogram.

• the chromosome coordinates labels.

• the circular barplot of number of deletions in each chromosome window.

• the circular barplot of number of duplications in each chromosome window.

• the circular barplot of number of inversions in each chromosome window.

Author(s)

Wen Yao

Examples

    delly <- readDelly(system.file("extdata/delly",package="intansv"))
    str(delly)

    load(system.file("extdata/genome.anno.RData",package="intansv"))
    str(genome)

    plotChromosome(genome,delly,1000000)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(intansv)
Loading required package: plyr
Loading required package: ggbio
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: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:plyr':

    rename

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:plyr':

    desc

Loading required package: GenomeInfoDb
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/intansv/plotChromosome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotChromosome
> ### Title: Display the chromosome distribution of structural variations
> ### Aliases: plotChromosome
> 
> ### ** Examples
> 
> 
>     delly <- readDelly(system.file("extdata/delly",package="intansv"))
>     str(delly)
List of 3
 $ del:'data.frame':	1208 obs. of  4 variables:
  ..$ chromosome: chr [1:1208] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : int [1:1208] 65580 86457 153671 172303 201850 208219 226809 230526 276053 276807 ...
  ..$ pos2      : num [1:1208] 65949 87419 153829 172439 201959 ...
  ..$ size      : num [1:1208] 369 962 158 136 109 358 104 128 129 143 ...
 $ dup:'data.frame':	29 obs. of  4 variables:
  ..$ chromosome: chr [1:29] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : int [1:29] 120788 910613 1133978 1614997 5696565 5757285 14472343 17377712 21630340 22551409 ...
  ..$ pos2      : num [1:29] 128008 911328 1136610 1616026 5699335 ...
  ..$ size      : num [1:29] 7220 715 2632 1029 2770 ...
 $ inv:'data.frame':	23 obs. of  4 variables:
  ..$ chromosome: chr [1:23] "chr05" "chr05" "chr05" "chr05" ...
  ..$ pos1      : int [1:23] 5550226 6942367 8700896 10402721 11062213 12014418 13291663 15092334 18737134 18770845 ...
  ..$ pos2      : num [1:23] 5550352 6944731 8702504 10402842 11631416 ...
  ..$ size      : num [1:23] 126 2364 1608 121 569203 ...
 - attr(*, "method")= chr "DELLY"
> 
>     load(system.file("extdata/genome.anno.RData",package="intansv"))
>     str(genome)
Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
  ..@ seqnames       :Formal class 'Rle' [package "IRanges"] with 4 slots
  .. .. ..@ values         : Factor w/ 2 levels "chr05","chr10": 1 2
  .. .. ..@ lengths        : int [1:2] 1 1
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. ..@ start          : int [1:2] 1 1
  .. .. ..@ width          : int [1:2] 29958434 23207287
  .. .. ..@ NAMES          : NULL
  .. .. ..@ elementType    : chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ strand         :Formal class 'Rle' [package "IRanges"] with 4 slots
  .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 3
  .. .. ..@ lengths        : int 2
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 2
  .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomicRanges"] with 4 slots
  .. .. ..@ seqnames   : chr [1:2] "chr05" "chr10"
  .. .. ..@ seqlengths : int [1:2] 29958434 23207287
  .. .. ..@ is_circular: logi [1:2] NA NA
  .. .. ..@ genome     : chr [1:2] NA NA
  ..@ metadata       : list()
> 
>     plotChromosome(genome,delly,1000000)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>