geom_chevron {ggbio} | R Documentation

## Chevron geoms for GRanges object

### Description

Break normal intervals stroed in `GRanges` object and show them as chevron, useful for showing model or splice summary.

### Usage

    ## S4 method for signature 'GRanges'
    geom_chevron(data, ..., xlab, ylab, main,
                 offset = 0.1,
                 facets = NULL,
                 stat = c("stepping", "identity"),
                 chevron.height.rescale = c(0.1, 0.8),
                 group.selfish = TRUE)

### Arguments

`data` | A GRanges object.
`...` | Extra parameters passed to autoplot function.
`xlab` | Label for x
`ylab` | Label for y
`main` | Title for plot.
`offset` | A nunmeric value or characters. If it's numeric value, indicate how much you want the chevron to wiggle, usually the rectangle for drawing `GRanges` is of height unit 1, so it's better between -0.5 and 0.5 to make it nice looking. Unless you specify offset as one of those columns, this will use height of the chevron to indicate the columns. Of course you could use size of the chevron to indicate the column variable easily, please see the examples.
`facets` | faceting formula to use.
`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`.
`chevron.height.rescale` | A numeric vector of length 2. When the offset parameters is a character which is one of the data columns, this parameter rescale the offset.
`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.

### Details

To draw a normal GRanges as Chevron, we need to provide a special geom for this purpose. Chevron is popular in gene viewer or genomoe browser, when they try to show isoforms or gene model.`geom_chevron`, just like any other `geom_*` function in ggplot2, you can pass aes() to it to use height of chevron or width of chevron to show statistics summary.

### 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_chevron()
    ## or
    ggplot() + geom_chevron(gr)

    ## ======================================================================
    ##  facetting and aesthetics
    ## ======================================================================
    ggplot(gr) + geom_chevron(facets = sample ~ seqnames, aes(color = strand))

    ## ======================================================================
    ##  stat:identity
    ## ======================================================================
    ggplot(gr) + geom_chevron(stat = "identity", aes(y = value))

    ## ======================================================================
    ##  stat:stepping
    ## ======================================================================
    ggplot(gr) + geom_chevron(stat = "stepping", aes(group = pair))

    ## ======================================================================
    ##  group.selfish controls when
    ## ======================================================================
    ggplot(gr) + geom_chevron(stat = "stepping", aes(group = pair), group.selfish = FALSE,
                            xlab = "xlab", ylab = "ylab", main = "main")

    p <- qplot(x = mpg, y = cyl, data = mtcars)

    ## ======================================================================
    ##  offset
    ## ======================================================================
    gr2 <- GRanges("chr1", IRanges(c(1, 10, 20), width = 5))
    gr2.p <- gaps(gr2)
    ## resize to connect them
    gr2.p <- resize(gr2.p, fix = "center", width = width(gr2.p)+2)

    ggplot(gr2) + geom_rect() + geom_chevron(gr2.p)

    ## notice the rectangle height is 0.8
    ## offset = 0 just like a line
    ggplot(gr2) + geom_rect() + geom_chevron(gr2.p, offset = 0)

    ## equal height
    ggplot(gr2) + geom_rect() + geom_chevron(gr2.p, offset = 0.4)

    ## ======================================================================
    ##  chevron.height
    ## ======================================================================
    values(gr2.p)$score <- c(100, 200)
    ggplot(gr2) + geom_rect() + geom_chevron(gr2.p, offset = "score")
    ## chevron.height
    ggplot(gr2) + geom_rect() + geom_chevron(gr2.p, offset = "score",
                                             chevron.height.rescale = c(0.4, 10))

[Package ggbio version 1.35.2 Index]