reverse_species_order

Returns an orthologs_df (data.frame) with reversed species order compared to the inputted orthologs_df.
sp1 becomes sp2 and the otherway around. It intends at facilitating the integration of more than just two datasets.
It outputs a data.frame shaped as following :
sp1.ID,sp1.Chr,sp1.Start,sp1.End,sp1.Index,sp2.ID,sp2.Chr,sp2.Start,sp2.End,sp2.Index

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.

Sami El Hilali

macrosyntR

Draw Ordered Oxford Grids and Chord Diagrams

Richard Copley

reverse_species_order function

<dl><dt>orthologs_df</dt>
<dd>orthologs_df dataframe. mutual best hits with genomic coordinates loaded with load_orthologs()</dd></dl>

Arguments

Reverse order of the species in an orthologs_df. — reverse_species_order

<dl>

<dt>orthologs_df</dt>
<dd>orthologs_df dataframe. mutual best hits with genomic coordinates loaded with load_orthologs()</dd>

</dl>

reverse_species_order: Reverse order of the species in an orthologs_df.

Description

Usage

Value

Arguments

See Also

Examples