addStepping-method: Adding disjoint levels to a GenomicRanges object

In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

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)

lawremi/biovizBase documentation built on Dec. 21, 2021, 9:42 a.m.