Last data update: 2014.03.03
R: Arch geoms for GRanges object
Arch geoms for GRanges object
Description
Show interval data as arches.
Usage
## S4 method for signature 'data.frame'
geom_arch(data, ..., n = 25, max.height = 10)
## S4 method for signature 'GRanges'
geom_arch(data, ..., xlab, ylab, main, facets = NULL,
rect.height = 0, n = 25, max.height = 10)
Arguments
data
A GRanges
or data.frame
object.
...
Extra parameters passed to autoplot function, aes
mapping
support height, x, xend
.
xstart of the arches
xendend of the arches
heightheight of arches
xlab
Label for x
ylab
Label for y
main
Title for plot.
n
Integer values at which interpolation takes place to create 'n'
equally spaced points spanning the interval ['min(x)', 'max(x)'].
facets
Faceting formula to use.
rect.height
When data is GRanges
, this padding the arches from original y
value to allow users putting arches 'around' the interval rectangles.
max.height
Max height of all arches.
Details
To draw a interval data as arches, we need to provide a special geom for
this purpose. Arches is popular in gene viewer or genomoe browser,
when they try to show isoforms or gene model.geom_arch
,
just like any other geom_*
function in ggplot2, you can pass
aes() to it to map variable to height of arches.
Value
A 'Layer'.
Author(s)
Tengfei Yin
Examples
set.seed(1)
N <- 100
library(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_arch()
# or
ggplot() + geom_arch(gr)
## =======================================
## facetting and aesthetics
## =======================================
ggplot(gr) + geom_arch(aes(color = value, height = value, size = value),
alpha = 0.2, facets = sample ~ seqnames)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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_arch-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geom_arch
> ### Title: Arch geoms for GRanges object
> ### Aliases: geom_arch geom_arch,data.frame-method geom_arch,GRanges-method
> ### geom_arch,missing-method geom_arch,uneval-method
>
> ### ** Examples
>
> set.seed(1)
> N <- 100
> library(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_arch()
> # or
> ggplot() + geom_arch(gr)
>
> ## =======================================
> ## facetting and aesthetics
> ## =======================================
> ggplot(gr) + geom_arch(aes(color = value, height = value, size = value),
+ alpha = 0.2, facets = sample ~ seqnames)
>
>
>
>
>
>
>
> dev.off()
null device
1
>