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Last data update: 2014.03.03

R: Add ideogram track

add_ideogram_track

R Documentation

Add ideogram track

Description

Add ideogram track

Usage

add_ideogram_track(cytoband = system.file("extdata", "cytoBand.txt",
    package = "circlize"), species = NULL, track = current_track() + 1)

Arguments

`cytoband`	Path of the cytoband file or a data frame that already contains cytoband data. Pass to `read.cytoband`.
`species`	Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download `cytoBand.txt.gz` from UCSC ftp automatically. Pass to `read.cytoband`.
`track`	which track the ideogram is added in. By default it is the next track in the layout.

Details

A track which contains ideograms will be added to the plot.

The function tries to download cytoband file from UCSC ftp. If there is no cytoband file available for the species, there will be an error.

Value

No value is returned.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

gtrellis_layout(n_track = 2, ncol = 3,
    track_height = unit.c(unit(1, "null"), unit(5, "mm")))
add_ideogram_track(track = 2)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(gtrellis)
Loading required package: grid
Loading required package: IRanges
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: 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: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/gtrellis/add_ideogram_track.rd_%03d_medium.png", width=480, height=480)
> ### Name: add_ideogram_track
> ### Title: Add ideogram track
> ### Aliases: add_ideogram_track
> 
> ### ** Examples
> 
> gtrellis_layout(n_track = 2, ncol = 3,
+     track_height = unit.c(unit(1, "null"), unit(5, "mm")))
> add_ideogram_track(track = 2)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>