ggbio (version 1.20.1)

geom_segment: Segment geoms for GRanges object

Description

Show interval data as segments.

Usage

## S3 method for class 'ANY':
geom_segment(data, ...)## S3 method for class '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'.

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))



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


## ======================================================================
##  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))


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


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