add_ideogram_track: Add ideogram track

In gtrellis: Genome Level Trellis Layout

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 <[e-mail]>

Examples

# There is no example
NULL

Example output

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, sd, var, xtabs

The following objects are masked from ‘package:base’:

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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
========================================
gtrellis version 1.22.0
Bioconductor page: http://bioconductor.org/packages/gtrellis/
Github page: https://github.com/jokergoo/gtrellis
Documentation: http://bioconductor.org/packages/gtrellis/

If you use it in published research, please cite:
Gu, Z. gtrellis: an R/Bioconductor package for making genome-level 
  Trellis graphics. BMC Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(gtrellis))
========================================

NULL

gtrellis documentation built on Nov. 8, 2020, 7:50 p.m.