Draw Ordered Oxford Grids and Chord Diagrams
Compute Linkage groups
Compute significant macrosynteny blocks
get the syntenic genes as a table
load orthologs with their genomic coordinates.
plot the Macro-synteny as a chord diagram
Plot Macro-synteny
plot the Macro-synteny as an oxford grid.
Reorder the mbh_df before plotting
Reorder the chromosomes of two or more species before plotting
Reverse order of the species in an orthologs_df.
Subset Orthologs contained in conserved linkage groups
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.