Segment geoms for GRanges object

Description

Show interval data as vertical bar, width equals to interval width and use 'score' or specified 'y' as y scale.

Usage

## S4 method for signature 'ANY'
geom_bar(data, ...)
## S4 method for signature 'GRanges'
geom_bar(data,..., xlab, ylab, main)

Arguments

Details

Useful for showing bed like files, when imported as GRanges, have a extra 'score' column, use it as default y, you could also specify y by using aes(y = ).

Value

A 'Layer'.

Examples

## load
library(GenomicRanges)

## simul
set.seed(123)
gr.b <- GRanges(seqnames = "chr1", IRanges(start = seq(1, 100, by = 10),
                  width = sample(4:9, size = 10, replace = TRUE)),
                score = rnorm(10, 10, 3), value = runif(10, 1, 100))
gr.b2 <- GRanges(seqnames = "chr2", IRanges(start = seq(1, 100, by = 10),
                  width = sample(4:9, size = 10, replace = TRUE)),
                score = rnorm(10, 10, 3), value = runif(10, 1, 100))
gr.b <- c(gr.b, gr.b2)
## default use score as y

## bar
ggplot(gr.b) + geom_bar(aes(fill = value))
## or
ggplot() + geom_bar(gr.b, aes(fill = value))
ggplot(gr.b) + geom_bar(aes(y = value))
## equal to
autoplot(gr.b, geom = "bar")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ggbio)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ggbio/geom_bar-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geom_bar
> ### Title: Segment geoms for GRanges object
> ### Aliases: geom_bar geom_bar,ANY-method geom_bar,GRanges-method
> ###   geom_bar,missing-method geom_bar,chevron-method
> 
> ### ** Examples
> 
> ## load
> library(GenomicRanges)
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> ## simul
> set.seed(123)
> gr.b <- GRanges(seqnames = "chr1", IRanges(start = seq(1, 100, by = 10),
+                   width = sample(4:9, size = 10, replace = TRUE)),
+                 score = rnorm(10, 10, 3), value = runif(10, 1, 100))
> gr.b2 <- GRanges(seqnames = "chr2", IRanges(start = seq(1, 100, by = 10),
+                   width = sample(4:9, size = 10, replace = TRUE)),
+                 score = rnorm(10, 10, 3), value = runif(10, 1, 100))
> gr.b <- c(gr.b, gr.b2)
Warning message:
In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
> ## default use score as y
> 
> ## bar
> ggplot(gr.b) + geom_bar(aes(fill = value))
use score as y by default
> ## or
> ggplot() + geom_bar(gr.b, aes(fill = value))
use score as y by default
> ggplot(gr.b) + geom_bar(aes(y = value))
> ## equal to
> autoplot(gr.b, geom = "bar")
use score as y by default
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>