About chromDraw

ChromDraw is a simple R package/console application for visualization of linear and circular karyotypes. The linear type of visualization is usually used for demonstrating chromosomes structures in the karyotype and the circular type of visualization is used for comparison of the karyotypes of different species.

ChromDraw requires two input files. First, the main input file/ input matrix containing definition of the karyotypes and marks. Second, file containing definitions of genomic blocks colors (in RGB). Output file formats are *.eps and *.svg. ChromDraw can visualize files in the  BED file format, that is requirement the first nine of fields per each record.

Main functionality of chromDraw was written in the C++ language. Graphic primitives are plotted by the C++ library BOARD.

In R the input matrix may be represented by the list of genomicRanges structures. The data of the colors may be represented by the data frame structure.

License:

GNU GPL-3

Download:

Links:

source code
R package for Linux
R binary package for Windows
LibBoard

Dependences:

  • R >= (3.0.0)
  • Rtools >= (3.1)
  • Rcpp >= (0.11.1)
  • GenomicRanges >= (1.17.46)

Install:

  • Install in R:

    • Install all dependences.
    • Download the package for Linux/Windows to your working directory.
    • In R type install.packages(“packageX.Y.Z.tar.gz”) , package = name of package with version number.
    • Or you can follow instruction on this page.

  • Install in Linux:

    • Download and install library Board.
    • In terminal change actual directory to the directory with source code of chromDraw.
    • Set INCLUDES and LIBDIRS to the path to the Libboard in the Makefile.
    • Type make and than you obtain binary file of chromDraw.

  • Install in Windows:

    • Download and install library Board.
    • Set INCLUDES and LIBDIRS to the path to the Libboard in the Makefile.
    • Use MinGW command prompt and type make in the directory with the source code.

Documentation:

Documentation for R package implementation you can download here.
Documentation for C++ implementation you can download here.

Online version:

Online limited version of chromDraw is available here.

Citation:

Janečka, Jan, and Martin A. Lysak. "chromDraw: an R package for visualization of linear and circular karyotypes." Chromosome Research (2015): 1-7.

Author:

Jan Janečka contact