R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Adding disjoint levels to a GenomicRanges object

addStepping-method

R Documentation

Adding disjoint levels to a GenomicRanges object

Description

Adding disjoint levels to a GenomicRanges object

Usage

## S4 method for signature 'GenomicRanges'
addStepping(obj, group.name, extend.size = 0,
                       fix = "center",
                       group.selfish = TRUE)

Arguments

`obj`	A GenomicRanges object
`group.name`	Column name in the elementMetadata which specify the grouping information of all the entries. If provided, this will make sure all intervals belong to the same group will try to be on the same level and nothing falls in between.
`extend.size`	Adding invisible buffered region to the GenomicRanges object, if it's 10, then adding 5 at both end. This make the close neighbors assigned to the different levels and make your eyes easy to identify.
`fix`	"start", "end", or "center"(default) passed to `resize`, denoting what to use as an anchor for each element of obj, and add extend.size to it's current width.
`group.selfish`	Passed to `addStepping`, control whether to show each group as unique level or not. If set to `FALSE`, if two groups are not overlapped with each other, they will probably be layout in the same level to save space.

Details

This is a tricky question, for example, pair-end RNA-seq data could be represented as two set of GenomicRanges object, one indicates the read, one indicates the junction. At the same time, we need to make sure pair-ended read are shown on the same level, and nothing falls in between. For better visualization of the data, we may hope to add invisible extended buffer to the reads, so closely neighbored reads will be on the different levels.

Value

A modified GenmicRanges object with stepping as one column.

Author(s)

Tengfei Yin

Examples

library(GenomicRanges)
set.seed(1)
N <- 500
## sample GRanges
gr <- GRanges(seqnames =
              sample(c("chr1", "chr2", "chr3", "chrX", "chrY"),
                     size = N, replace = TRUE),
              IRanges(
                      start = sample(1:300, size = N, replace = TRUE),
                      width = sample(70:75, size = N,replace = TRUE)),
              strand = sample(c("+", "-", "*"), size = N,
                replace = TRUE),
              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
              group = sample(c("Normal", "Tumor"),
                size = N, replace = TRUE),
              pair = sample(letters, size = N,
                replace = TRUE))

## grouping and extending
head(addStepping(gr))
head(addStepping(gr, group.name = "pair"))
gr.close <- GRanges(c("chr1", "chr1"), IRanges(c(10, 20), width = 9))
addStepping(gr.close)
addStepping(gr.close, extend.size = 5)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(biovizBase)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biovizBase/addStepping-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addStepping-method
> ### Title: Adding disjoint levels to a GenomicRanges object
> ### Aliases: addStepping addStepping,GenomicRanges-method
> 
> ### ** Examples
> 
> library(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
> set.seed(1)
> N <- 500
> ## sample GRanges
> gr <- GRanges(seqnames =
+               sample(c("chr1", "chr2", "chr3", "chrX", "chrY"),
+                      size = N, replace = TRUE),
+               IRanges(
+                       start = sample(1:300, size = N, replace = TRUE),
+                       width = sample(70:75, size = N,replace = TRUE)),
+               strand = sample(c("+", "-", "*"), size = N,
+                 replace = TRUE),
+               value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
+               group = sample(c("Normal", "Tumor"),
+                 size = N, replace = TRUE),
+               pair = sample(letters, size = N,
+                 replace = TRUE))
> 
> ## grouping and extending
> head(addStepping(gr))
GRanges object with 6 ranges and 5 metadata columns:
       seqnames     ranges strand |     value     score       group        pair
          <Rle>  <IRanges>  <Rle> | <numeric> <numeric> <character> <character>
  chr1     chr1 [241, 313]      * |  8.120639 102.31909       Tumor           n
  chr1     chr1 [ 54, 126]      + |  7.493114  64.50273       Tumor           w
  chr1     chr1 [273, 343]      - | 13.374793  87.88790      Normal           m
  chr1     chr1 [138, 207]      * |  9.951429  87.32883      Normal           p
  chr1     chr1 [ 25,  99]      + | 12.831509 111.22355      Normal           z
  chr1     chr1 [ 33, 103]      * | 12.346409 108.72000       Tumor           m
        stepping
       <numeric>
  chr1         2
  chr1        29
  chr1         9
  chr1        18
  chr1        20
  chr1        21
  -------
  seqinfo: 5 sequences from an unspecified genome; no seqlengths
> head(addStepping(gr, group.name = "pair"))
GRanges object with 6 ranges and 5 metadata columns:
       seqnames     ranges strand |     value     score       group        pair
          <Rle>  <IRanges>  <Rle> | <numeric> <numeric> <character> <character>
  chr1     chr1 [241, 313]      * |  8.120639 102.31909       Tumor           n
  chr1     chr1 [ 54, 126]      + |  7.493114  64.50273       Tumor           w
  chr1     chr1 [273, 343]      - | 13.374793  87.88790      Normal           m
  chr1     chr1 [138, 207]      * |  9.951429  87.32883      Normal           p
  chr1     chr1 [ 25,  99]      + | 12.831509 111.22355      Normal           z
  chr1     chr1 [ 33, 103]      * | 12.346409 108.72000       Tumor           m
        stepping
       <numeric>
  chr1        14
  chr1        22
  chr1        13
  chr1        16
  chr1        25
  chr1        13
  -------
  seqinfo: 5 sequences from an unspecified genome; no seqlengths
> gr.close <- GRanges(c("chr1", "chr1"), IRanges(c(10, 20), width = 9))
> addStepping(gr.close)
GRanges object with 2 ranges and 1 metadata column:
       seqnames    ranges strand |  stepping
          <Rle> <IRanges>  <Rle> | <numeric>
  chr1     chr1  [10, 18]      * |         1
  chr1     chr1  [20, 28]      * |         1
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> addStepping(gr.close, extend.size = 5)
GRanges object with 2 ranges and 1 metadata column:
       seqnames    ranges strand |  stepping
          <Rle> <IRanges>  <Rle> | <numeric>
  chr1     chr1  [10, 18]      * |         1
  chr1     chr1  [20, 28]      * |         2
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>