R: Calculate stepping levels

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()

plot of chunk unnamed-chunk-1

## or
ggplot() + stat_stepping(gr)

plot of chunk unnamed-chunk-1

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

plot of chunk unnamed-chunk-1

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

plot of chunk unnamed-chunk-1

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

[Package ggbio version 1.5.20 ]