macrosyntR

CRANmacrosyntRMaRDI QIDQ60405FDOQ60405

Draw Ordered Oxford Grids and Chord Diagrams

Sami El Hilali, Richard R Copley

Last update: 14 November 2023

Copyright license: GNU General Public License, version 3.0

Software version identifier: 0.2.19, 0.2.14, 0.3.3

Description

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.

Cites work

• Deeply conserved synteny and the evolution of metazoan chromosomes
• Deeply conserved synteny resolves early events in vertebrate evolution
• The Oxford Grid
• Finding community structure in very large networks

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