stat_stepping-method: Calculate stepping levels

In tengfei/ggbio: Visualization tools for genomic data

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")

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.