stat_stepping {ggbio} | R Documentation

## Calculate stepping levels

### Description

Calculate stepping levels.

### Usage

    ## S4 method for signature 'GRanges'
    stat_stepping(data, ..., xlab, ylab, main,
                  facets = NULL,
                  geom = c("rect", "alignment", "segment"))

### Arguments

`data` | A `GRanges` or `data.frame` object.
`...` | Extra parameters such as aes() passed to `geom_rect`, `geom_alignment`, or `geom_segment`.
`xlab` | Label for x
`ylab` | Label for y
`main` | Title for plot.
`facets` | Faceting formula to use.
`geom` | The geometric object used to display the data. For 'stepping', could be one of 'rect', 'alignment', 'segment'.

### Value

A 'Layer'.

### Author(s)

Tengfei Yin

### Examples

    set.seed(1)
    N <- 50

    require(GenomicRanges)
    ##  simul
    ## ======================================================================
    ##  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) + stat_stepping()
    ## or
    ggplot() + stat_stepping(gr)

    ##  facet_aes
    ggplot(gr) + stat_stepping(aes(color = strand, fill = strand),
                                     facets = sample ~ seqnames)

    ##  geom_segment
    ggplot(gr) + stat_stepping(aes(color = strand),
                             geom = "segment", xlab = "Genomic coord", ylab = "y", main = "hello")

    ##  geom_alignment
    ## ggplot(gr) + stat_stepping(geom = "alignment")

    ##  geom_alignment_group
    ##  ggplot(gr) + stat_stepping(aes(group = pair),geom = "alignment")

[Package ggbio version 1.28.5 Index]