stat_reduce-method: Reduce an object.

In ggbio: Visualization tools for genomic data

Description

Reduce GRanges, IRanges or TxDb object.

Usage

## S4 method for signature 'GRanges'
stat_reduce(data, ...,
           xlab, ylab, main,
           drop.empty.ranges = FALSE,
           min.gapwidth = 1L,
           facets = NULL, geom = NULL)

## S4 method for signature 'IRanges'
stat_reduce(data, ...,
           xlab, ylab, main,
           drop.empty.ranges = FALSE,
           min.gapwidth = 1L,
           with.inframe.attrib=FALSE,
           facets = NULL, geom = NULL)

## S4 method for signature 'TxDbOREnsDb'
stat_reduce(data, ...)

Arguments

data	GRanges, IRanges or TxDb object.
...	passed to aesthetics mapping.
xlab	x label.
ylab	y label.
main	title.
drop.empty.ranges	pass to reduce function.
min.gapwidth	pass to reduce function.
with.inframe.attrib	pass to reduce function.
facets	pass to reduce function.
geom	geometric type.

Value

a ggplot object.

Author(s)

Tengfei Yin

See Also

reduce.

Examples

set.seed(1)
N <- 1000
library(GenomicRanges)

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))

ggplot(gr) + stat_reduce()
autoplot(gr, stat = "reduce")
strand(gr) <- "*"
ggplot(gr) + stat_reduce()

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
data(genesymbol, package = "biovizBase")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
## made a track comparing full/reduce stat.
ggplot(txdb) + stat_reduce(which = genesymbol["RBM17"])

ggbio documentation built on Nov. 8, 2020, 5:04 p.m.