macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams
Use standard genomics file format (BED) and a table of orthologs to illustrate synteny conservation at the genome-wide scale. Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z> and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>. The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>) and so automatically order the chromosomes on the plot to improve interpretability.
| Version: | 0.3.3 |
| Depends: | R (≥ 4.1.0) |
| Imports: | stats, utils,ggplot2,igraph,tidyr,reshape2,dplyr,stringr,rlang |
| Suggests: | knitr,rmarkdown |
| Published: | 2023-11-14 |
| DOI: | 10.32614/CRAN.package.macrosyntR |
| Author: | Sami El Hilali [aut, cre], Richard Copley [aut] |
| Maintainer: | Sami El Hilali <elhilali.sami at gmail.com> |
| BugReports: | https://github.com/SamiLhll/macrosyntR/issues |
| License: | GPL-3 |
| URL: | https://github.com/SamiLhll/macrosyntR |
| NeedsCompilation: | no |
| Citation: | macrosyntR citation info |
| Materials: | README,NEWS |
| CRAN checks: | macrosyntR results |
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