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chromDraw: an R package for visualization of linear and circular karyotypes

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Abstract

Species-specific sets of chromosomes—karyotypes—are traditionally depicted as linear ideograms with individual chromosomes represented by vertical bars. However, linear visualization has its limitations when the shared collinearity and/or chromosomal rearrangements differentiating two or more karyotypes need to be demonstrated. In these instances, circular visualization might provide easier comprehension and interpretation of inter-species chromosomal collinearity. The chromDraw graphical tool was developed as a user-friendly graphical tool for visualizing both linear and circular karyotypes based on the same input data matrix. The output graphics, saved in two different formats (EPS and SVG), can be easily imported to and modified in presentation and image-editing computer programs. The tool is freely distributed under GNU General Public License (GPL) and can be installed from Bioconductor or from the chromDraw home page.

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Abbreviations

BED:

Browser Extensible Display

C++:

Programming language

EPS:

Encapsulated PostScript

GPL:

General Public License

R:

Programming language and software environment

rDNA:

Ribosomal DNA

RGB:

Red, green, blue

SVG:

Scalable Vector Graphic

References

  • Bioconductor PM (2014) BiocCheck: Bioconductor-specific package checks. [Software]. R package version 1.1.9

  • Chen H, Wang X (2013) CrusView: a java-based visualization platform for comparative genomics analyses in brassicaceae species. Plant Physiol 163:354–362

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dohi H, Ishizuka M, Minoshima S, Shimizu N (1993) GeneView: multi-language human gene mapping library with a graphical user interface. CABIOS 9:459–464

    CAS  PubMed  Google Scholar 

  • Eddelbuettel D, François R, Allaire J, Chambers J, Bates D, Ushey K (2011) Rcpp: Seamless R and C++ integration. J Stat Softw 40:1–18

    Google Scholar 

  • Fourey S (2014) LibBoard: a vector graphics C++ library (Version 0.9.0). [Software]. GREYC Laboratory

  • Fukui K (1986) Standardization of karyotyping plant chromosomes by a newly developed chromosome image analyzing system (CHIAS). Theor Appl Genet 72:27–32

    Article  CAS  PubMed  Google Scholar 

  • Fukui K, Iijima K (1991) Somatic chromosome map of rice by imaging methods. Theor Appl Genet 81:589–596

    Article  CAS  PubMed  Google Scholar 

  • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80

    Article  PubMed  PubMed Central  Google Scholar 

  • Guy L, Kultima JR, Andersson SG (2010) genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26:2334–2335

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Care VJ (2013) Software for computing and annotating genomic ranges. PLoS Comput Biol 9, e1003118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lyons E, Freeling M (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53:661–673

    Article  CAS  PubMed  Google Scholar 

  • Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA (2010) Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell Online 22:2277–2290

    Article  Google Scholar 

  • Mandáková T, Schranz ME, Sharbel TF, Jong H, Lysak MA (2015) Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes. Plant J 82:785–793

    Article  PubMed  Google Scholar 

  • Pook S, Vaysseix G, Barillot E (1998) Zomit: biological data visualization and browsing. Bioinformatics 14:807–814

    Article  CAS  PubMed  Google Scholar 

  • Schranz ME, Lysak MA, Mitchell-Olds T (2006) The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535–542

    Article  CAS  PubMed  Google Scholar 

  • Tenenbaum D, Team B (2014) BiocInstaller: Install/Update Bioconductor and CRAN Packages. [Software]. R package version 1.15.5

  • Yin T, Cook D, Lawrence M (2012) ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology 13: R77

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Acknowledgments

We thank Dr Terezie Mandáková and Petra Hloušková for helpful suggestions and comments on the functionality of the chromDraw package. Drs Matej Lexa and Jiří Hon are acknowledged for ideas on how to expand the package and for introduction to the R world, respectively. This research was supported by a grant from the Czech Science Foundation (P501/12/G090) and by European Social Fund (CZ.1.07/2.3.00/20.0189).

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Correspondence to Martin A. Lysak.

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Responsible Editor: Hans de Jong

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Janečka, J., Lysak, M.A. chromDraw: an R package for visualization of linear and circular karyotypes. Chromosome Res 24, 217–223 (2016). https://doi.org/10.1007/s10577-015-9513-5

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  • DOI: https://doi.org/10.1007/s10577-015-9513-5

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