geom_arrowrect {ggbio}R Documentation

Arrowrect geoms for GRanges object

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()

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## or
ggplot() + geom_arrowrect(gr)

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

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

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

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

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[Package ggbio version 1.5.20 ]