Advertisement

Chromosome Research

, Volume 24, Issue 2, pp 217–223 | Cite as

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

  • Jan Janečka
  • Martin A. LysakEmail author
Article

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.

Keywords

Visualization Chromosome Karyotype 

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

Notes

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).

References

  1. Bioconductor PM (2014) BiocCheck: Bioconductor-specific package checks. [Software]. R package version 1.1.9Google Scholar
  2. Chen H, Wang X (2013) CrusView: a java-based visualization platform for comparative genomics analyses in brassicaceae species. Plant Physiol 163:354–362CrossRefPubMedPubMedCentralGoogle Scholar
  3. Dohi H, Ishizuka M, Minoshima S, Shimizu N (1993) GeneView: multi-language human gene mapping library with a graphical user interface. CABIOS 9:459–464PubMedGoogle Scholar
  4. Eddelbuettel D, François R, Allaire J, Chambers J, Bates D, Ushey K (2011) Rcpp: Seamless R and C++ integration. J Stat Softw 40:1–18Google Scholar
  5. Fourey S (2014) LibBoard: a vector graphics C++ library (Version 0.9.0). [Software]. GREYC LaboratoryGoogle Scholar
  6. Fukui K (1986) Standardization of karyotyping plant chromosomes by a newly developed chromosome image analyzing system (CHIAS). Theor Appl Genet 72:27–32CrossRefPubMedGoogle Scholar
  7. Fukui K, Iijima K (1991) Somatic chromosome map of rice by imaging methods. Theor Appl Genet 81:589–596CrossRefPubMedGoogle Scholar
  8. 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:R80CrossRefPubMedPubMedCentralGoogle Scholar
  9. Guy L, Kultima JR, Andersson SG (2010) genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26:2334–2335CrossRefPubMedPubMedCentralGoogle Scholar
  10. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645CrossRefPubMedPubMedCentralGoogle Scholar
  11. 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, e1003118CrossRefPubMedPubMedCentralGoogle Scholar
  12. Lyons E, Freeling M (2008) How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 53:661–673CrossRefPubMedGoogle Scholar
  13. Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA (2010) Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell Online 22:2277–2290CrossRefGoogle Scholar
  14. 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 82:785–793CrossRefPubMedGoogle Scholar
  15. Pook S, Vaysseix G, Barillot E (1998) Zomit: biological data visualization and browsing. Bioinformatics 14:807–814CrossRefPubMedGoogle Scholar
  16. 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 11:535–542CrossRefPubMedGoogle Scholar
  17. Tenenbaum D, Team B (2014) BiocInstaller: Install/Update Bioconductor and CRAN Packages. [Software]. R package version 1.15.5Google Scholar
  18. Yin T, Cook D, Lawrence M (2012) ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology 13: R77Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.CEITEC-Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic

Personalised recommendations