geom_segment-method: Segment geoms for GRanges object

In ggbio: Visualization tools for genomic data

Description

Show interval data as segments.

Usage

## S4 method for signature 'ANY'
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))



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

ggbio documentation built on Nov. 8, 2020, 5:04 p.m.