geom_rect {ggbio} | R Documentation

## Rect geoms for GRanges object

### Description

Show interval data as rectangle.

### Usage

    ## S4 method for signature 'ANY'
    geom_rect(data, ...)
    ## S4 method for signature 'GRanges'
    geom_rect(data,..., xlab, ylab, main,
              facets = NULL, stat = c("stepping", "identity"),
              rect.height = NULL,
              group.selfish = TRUE)

### Arguments

`data` | Typically a `GRanges` or `data.frame` object. When it's `data.frame`, it's simply calling ggplot2::geom_rect.
`...` | Extra parameters such as aes() or `color, size` passed.
`xlab` | Label for x
`ylab` | Label for y
`main` | Title for plot.
`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`.
`rect.height` | Half height 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))

    ## ======================================================================
    ##  data.frame call ggplot2::geom_rect
    ## ======================================================================
    ggplot() + geom_rect(data = mtcars, aes(xmin = mpg, ymin = wt, xmax = mpg + 10, ymax = wt + 0.2,
                           fill = cyl))

    ## ======================================================================
    ##  default
    ## ======================================================================
    ggplot(gr) + geom_rect()
    # or
    ggplot() + geom_rect(gr)

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

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

    ## ======================================================================
    ##  stat:stepping
    ## ======================================================================
    ggplot(gr) + geom_rect(stat = "stepping", aes(y = value, group = pair))

    ## ======================================================================
    ##  group.selfish controls when
    ## ======================================================================
    ggplot(gr) + geom_rect(stat = "stepping", aes(y = value, group = pair), group.selfish = FALSE)

[Package ggbio version 1.26.1 Index]