plot_macrosynteny

This is a function to generate the contingency table of an MBH dataframe and apply fischer test to calculate the significant associations.

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

plot_macrosynteny function

<dl><dt>macrosynt_df</dt>
<dd>dataframe of contingency table with p-values calculated by the compute_macrosynteny() function</dd>
<dt>sp1_label</dt>
<dd>character. The name of the species1 to display on the plot</dd>
<dt>sp2_label</dt>
<dd>character. The name of the species2 to put on the plot</dd></dl>

Arguments

Plot Macro-synteny — plot_macrosynteny

<dl>

<dt>macrosynt_df</dt>
<dd>dataframe of contingency table with p-values calculated by the compute_macrosynteny() function</dd>


<dt>sp1_label</dt>
<dd>character. The name of the species1 to display on the plot</dd>


<dt>sp2_label</dt>
<dd>character. The name of the species2 to put on the plot</dd>

</dl>

plot_macrosynteny: Plot Macro-synteny

Description

Usage

Value

Arguments

See Also

Examples