R: Segment geoms for GRanges object

geom_segment {ggbio}

R Documentation

Segment geoms for GRanges object

Description

Show interval data as segments.

Usage

##  for data.frame
## S4 method for signature 'data.frame'
geom_segment(data, ...)

## S4 method for signature 'GRanges'
geom_segment(data,..., xlab, ylab, main,
          facets = NULL, stat = c("stepping", "identity"),
          group.selfish = TRUE)

Arguments

`data`	A `GRanges` or `data.frame` object.
`...`	Extra parameters such as aes() or `color, size` passed.
`xlab`	Label for x
`ylab`	Label for y
`main`	Title for plot.
`facets`	Faceting formula to use.
`stat`	Character vector specifying statistics to use. "stepping" with randomly assigned stepping levels as y varialbe. "identity" allow users to specify `y` value in `aes`.
`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.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

set.seed(1)
N <- 100
require(GenomicRanges)
## ======================================================================
##  simmulated GRanges
## ======================================================================
gr <- GRanges(seqnames = 
              sample(c("chr1", "chr2", "chr3"),
                     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),
              sample = sample(c("Normal", "Tumor"), 
                size = N, replace = TRUE),
              pair = sample(letters, size = N, 
                replace = TRUE))
## ======================================================================
##  data.frame call ggplot2::geom_segment
## ======================================================================
ggplot() + geom_segment(data = mtcars, aes(x = mpg, y = wt, xend = mpg + 10, yend = wt + 0.2,
                       fill = cyl))

plot of chunk unnamed-chunk-1

## ======================================================================
##  default
##
##  ======================================================================
ggplot(gr) + geom_segment()

plot of chunk unnamed-chunk-1

## or
ggplot() + geom_segment(gr)

plot of chunk unnamed-chunk-1

## ======================================================================
##  facetting and aesthetics
## ======================================================================
ggplot(gr) + geom_segment(facets = sample ~ seqnames, aes(color = strand, fill = strand))

## ======================================================================
##  stat:identity
## ======================================================================
ggplot(gr) + geom_segment(stat = "identity", aes(y = value))

plot of chunk unnamed-chunk-1

## ======================================================================
##  stat:stepping
## ======================================================================
ggplot(gr) + geom_segment(stat = "stepping", aes(y = value, group = pair))

plot of chunk unnamed-chunk-1

## ======================================================================
##  group.selfish controls when 
## ======================================================================
ggplot(gr) + geom_segment(stat = "stepping", aes(y = value, group = pair), group.selfish = FALSE)

plot of chunk unnamed-chunk-1

[Package ggbio version 1.5.20 ]