Last data update: 2014.03.03

 R: Display structural variations in a specific genomic region
plotRegionR Documentation

Display structural variations in a specific genomic region

Description

Display the structural variations in a specific genomic region in circular view.

Usage

    plotRegion(structuralVariation, genomeAnnotation, 
               regionChromosome, regionStart, regionEnd)

Arguments

structuralVariation

A list of structural variations.

genomeAnnotation

A genomic ranges of the genome annotation.

regionChromosome

The chromosome identifier of a specific region to view.

regionStart

The start coordinate of a specific region to view.

regionEnd

The end coordinate of a specific region to view.

Details

Different SVs were shown as rectangles in different layers. See the package vignette and the example dataset for more details.

Value

A circular plot of all the structural variations and genes in a specific region with four layers:

  • The composition of genes of a specific genomic region.

  • The composition of deletions of a specific genomic region.

  • The composition of duplications of a specific genomic region.

  • The composition of inversions of a specific genomic region.

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(msu_gff_v7)

    plotRegion(delly,msu_gff_v7,"chr05",1,200000)

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/plotRegion.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotRegion
> ### Title: Display structural variations in a specific genomic region
> ### Aliases: plotRegion
> 
> ### ** 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(msu_gff_v7)
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] 67758 45813
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. ..@ start          : int [1:113571] 4003 4003 4003 4003 6935 6935 6935 7271 8050 6935 ...
  .. .. ..@ width          : int [1:113571] 354 354 354 354 2165 2165 234 408 1050 234 ...
  .. .. ..@ NAMES          : NULL
  .. .. ..@ elementType    : chr "integer"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ strand         :Formal class 'Rle' [package "IRanges"] with 4 slots
  .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ...
  .. .. ..@ lengths        : int [1:4120] 12 4 4 38 29 76 12 188 76 32 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 113571
  .. .. ..@ listData       :List of 8
  .. .. .. ..$ source: Factor w/ 1 level "MSU_osa1r7": 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ type  : Factor w/ 6 levels "CDS","exon","five_prime_UTR",..: 4 5 2 1 4 5 2 2 2 1 ...
  .. .. .. ..$ score : num [1:113571] NA NA NA NA NA NA NA NA NA NA ...
  .. .. .. ..$ phase : int [1:113571] NA NA NA NA NA NA NA NA NA NA ...
  .. .. .. ..$ ID    : chr [1:113571] "LOC_Os05g00988" "LOC_Os05g00988.1" "LOC_Os05g00988.1:exon_1" "LOC_Os05g00988.1:cds_1" ...
  .. .. .. ..$ Name  : chr [1:113571] "LOC_Os05g00988" "LOC_Os05g00988.1" NA NA ...
  .. .. .. ..$ Note  :Formal class 'CompressedCharacterList' [package "IRanges"] with 5 slots
  .. .. .. .. .. ..@ elementType    : chr "character"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. .. ..@ partitioning   :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
  .. .. .. .. .. .. .. ..@ end            : int [1:113571] 1 1 1 1 2 2 2 2 2 2 ...
  .. .. .. .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. .. ..@ unlistData     : chr [1:8082] "hypothetical protein" "retrotransposon protein, putative, unclassified, expressed" "expressed protein" "expressed protein" ...
  .. .. .. ..$ Parent:Formal class 'CompressedCharacterList' [package "IRanges"] with 5 slots
  .. .. .. .. .. ..@ elementType    : chr "character"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. .. ..@ partitioning   :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
  .. .. .. .. .. .. .. ..@ end            : int [1:113571] 0 1 2 3 3 4 5 6 7 8 ...
  .. .. .. .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. .. ..@ unlistData     : chr [1:105489] "LOC_Os05g00988" "LOC_Os05g00988.1" "LOC_Os05g00988.1" "LOC_Os05g00990" ...
  .. .. ..@ 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] NA NA
  .. .. ..@ is_circular: logi [1:2] NA NA
  .. .. ..@ genome     : chr [1:2] NA NA
  ..@ metadata       : list()
> 
>     plotRegion(delly,msu_gff_v7,"chr05",1,200000)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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