stat_reduce {ggbio}R Documentation

Reduce an object.

Description

Reduce GRanges, IRanges or TranscriptDb 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 'TranscriptDb'
stat_reduce(data, ...)

Arguments

data

GRanges, IRanges or TranscriptDb 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()

plot of chunk unnamed-chunk-1 

autoplot(gr, stat = "reduce")

plot of chunk unnamed-chunk-1 

strand(gr) <- "*"
ggplot(gr) + stat_reduce()

plot of chunk unnamed-chunk-1 

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"])

## Aggregating TranscriptDb...

## Parsing exons...

## Parsing cds...

## Parsing transcripts...

## Aggregating...

## Done

## Constructing graphics...

plot of chunk unnamed-chunk-1

[Package ggbio version 1.5.20 ]