geom_arrow-method: Arrow geoms for GRanges object

In tengfei/ggbio: Visualization tools for genomic data

Arrow geoms for GRanges object

Description

Show interval data as arrows.

Usage

## S4 method for signature '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'.

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_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, length = unit(0.3, "cm"), angle = 45,
                      group.selfish = FALSE)

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.