R: Arch geoms for GRanges object

geom_arch {ggbio}

R Documentation

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)

plot of chunk unnamed-chunk-1

[Package ggbio version 1.5.20 ]