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)

[Package ggbio version 1.28.5 Index]