scale: get x scale breaks and labels

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

Description

get x scale breaks and labels for GRanges with different coordintes(currently only "truncate_gaps" and "genome" supported).

Usage

 ## S4 method for signature 'GRanges'
getXScale(obj, type = c("default", "all", "left", "right"))

Arguments

obj	a GRanges object. "coord" in metadata shows proper coordinates transformation for this object.
type	types of labels for transformed data.

Value

list of breaks and labels.

Author(s)

Tengfei Yin

Examples

library(GenomicRanges)
gr1 <- GRanges("chr1", IRanges(start = c(100, 300, 600),
                               end = c(200, 400, 800)))
shrink.fun1 <- shrinkageFun(gaps(gr1), max.gap = maxGap(gaps(gr1), 0.15))
shrink.fun2 <- shrinkageFun(gaps(gr1), max.gap = 0)
s1 <- shrink.fun1(gr1)
getXScale(s1)
#  coord:genome
set.seed(1)
gr1 <- GRanges("chr1", IRanges(start = as.integer(runif(20, 1, 100)),
width = 5))
gr2 <- GRanges("chr2", IRanges(start = as.integer(runif(20, 1, 100)),
width = 5))
gr <- c(gr1, gr2)
gr.t <- transformToGenome(gr, space.skip = 1)
getXScale(gr.t)

jotsetung/biovizBase documentation built on May 31, 2019, 11:43 p.m.