geom_arrowrect-method: Arrowrect geoms for GRanges object

In ggbio: Visualization tools for genomic data

Description

Show interval data as rectangle with a arrow head.

Usage

## S4 method for signature 'GRanges'
geom_arrowrect(data, ..., xlab, ylab, main,
              facets = NULL, stat = c("stepping", "identity"),
              rect.height = NULL, arrow.head = 0.06,
              arrow.head.rate = arrow.head,  arrow.head.fix = NULL,
              group.selfish = TRUE)

Arguments

data	A GRanges object.
...	Extra parameters such as aes() 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.
rect.height	Half height of the arrow body.
arrow.head	Arrow head to body ratio.
arrow.head.rate	Arrow head to body ratio. same with arrow.head.
arrow.head.fix	fixed length of arrow head.
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))


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

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


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


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


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

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