ggbio (version 1.20.1)

geom_arrow: Arrow geoms for GRanges object

Description

Show interval data as arrows.

Usage

## S3 method for class 'GRanges':
geom_arrow(data, ..., xlab, ylab, main,
          angle = 30, length = unit(0.12, "cm"), type = "open",
          stat = c("stepping", "identity"), facets = NULL,
          arrow.rate = 0.03, 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.

angle

The angle of the arrow head in degrees (smaller numbers produce narrower, pointier arrows). Essentially describes the width of the arrow head.

length

A unit specifying the length of the arrow head (from tip to base).

type

One of "open" or "closed" indicating whether the arrow head should be a closed triangle.

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.

facets

Faceting formula to use.

arrow.rate

Arrow density of the arrow body.

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))


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

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

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


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

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



## ======================================================================
## other options to control arrow angle, density, ...
## ======================================================================
library(grid)
ggplot(gr) + geom_arrow(stat = "stepping", aes(y = value, group = pair),
                      arrow.rate = 0.01, legnth = unit(0.3, "cm"), agnle = 45,
                      group.selfish = FALSE)