subset_linkage_orthologs

This is a function to subset an orthologs_df and keep only the orthologs that are within significant
linkage groups computed by the function compute_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.

Sami El Hilali

macrosyntR

Draw Ordered Oxford Grids and Chord Diagrams

Richard Copley

subset_linkage_orthologs function

<dl><dt>orthologs_df</dt>
<dd>dataframe. orthologs with genomic coordinates loaded with load_orthologs()</dd>
<dt>linkages</dt>
<dd>dataframe. table listing the linkage groups as returned by the function compute_linkage_groups()</dd></dl>

Arguments

Subset Orthologs contained in conserved linkage groups — subset_linkage_orthologs

<dl>

<dt>orthologs_df</dt>
<dd>dataframe. orthologs with genomic coordinates loaded with load_orthologs()</dd>


<dt>linkages</dt>
<dd>dataframe. table listing the linkage groups as returned by the function compute_linkage_groups()</dd>

</dl>

subset_linkage_orthologs: Subset Orthologs contained in conserved linkage groups

Description

Usage

Value

Arguments

See Also

Examples