chromDraw-package: chromDraw - simple karyotype visualization tool.

In chromDraw: chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.

Description

ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.

Details

Package:	chromDraw
Type:	Package
Date:	2015-12-12
License:	GPL-3
License:	LGPL | library Board

This package has only one function with two parameters, such as main function in C. First parameter ARGC is a count of input parameters and second parameter ARGV is vector contain calling parameters. Example: chromDraw(argc=5, argv=c("chromDraw", "-c", "/home/user/Documents/colors.txt", "-d", "/home/user/Documents/input_data.txt"))

First string in vector with arguments must be package name. The others strings in vector are parameter string and string with parameter value. As shown in the example.

Author(s)

Jan Janecka, Ing. Mgr. CEITEC MU Masaryk University Kamenice 5, Building A26 CZ-625 00, Brno Czech Republic tel.: [phone]

Email: [e-mail]

References

LibBoard: A vector graphics C++ library (Version 0.9.0). GREYC laboratory. [Software]. http://libboard.sourceforge.net/. [accessed Sept. 2014].

See Also

chromDraw main_chromDraw

Examples

OUTPUTPATH = file.path(getwd());
INPUTPATH = system.file('extdata','Ack_and_Stenopetalum_nutans.txt', package ='chromDraw')
COLORPATH = system.file('extdata','default_colors.txt', package ='chromDraw')
chromDraw(argc=7, argv=c("chromDraw", "-c", COLORPATH, "-d", INPUTPATH, "-o", OUTPUTPATH));

Example output

[1] 0

chromDraw documentation built on Nov. 8, 2020, 5:30 p.m.