getXScale {biovizBase}R Documentation

get x scale breaks and labels

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)
[Package biovizBase version 1.34.1 Index]