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Last data update: 2014.03.03

R: Arrow geoms for GRanges object

geom_arrow

R Documentation

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, legnth = unit(0.3, "cm"), agnle = 45,
                      group.selfish = FALSE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(ggbio)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ggbio/geom_arrow-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geom_arrow
> ### Title: Arrow geoms for GRanges object
> ### Aliases: geom_arrow geom_arrow,GRanges-method geom_arrow,missing-method
> ###   geom_arrow,uneval-method
> 
> ### ** Examples
> 
> set.seed(1)
> N <- 100
> require(GenomicRanges)
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> ## ======================================================================
> ##  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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>