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macrosyntR 0.3.3

Enhancements :

• removed dependency on ggthemes package that is scheduled for archival.

macrosyntR 0.3.1

New features :

• Two species and more can now be visualized on a chord diagram using the function plot_chord_diagram()

Enhancements :

• Redundant chromosome names from one species to another are now accepted

• load_orthologs now handles more than two species. It uses the argument ‘bedfiles’ instead of sp1_bed and sp2_bed which are still working when used together.

macrosyntR 0.2.21

Enhancements :

• added control when chromosome names are redundant in the ‘orthologs_df’ provided to ‘reorder_macrosynteny()’. It now raises an error with explanations about what’s wrong.

macrosyntR 0.2.19

New features :

• created the function get_syntenic_genes(). It takes an orthologs_df as input and outputs a table with the details of all detected blocks of two or more consecutive genes.

• created the function reverse_species_order(). It takes an orthologs_df as input and outputs it with sp1 changed in sp2 and the other way around. It can be called in plot_oxford_grid().

• Added the argument keep_sp1_raw_order in reorder_macrosynteny(). When set to TRUE, it returns an orthologs_df with only the sp2.Chr reordered, and doesn’t change the order of sp1.Chr compared with the input data. It can be also be called in plot_oxford_grid().

• ‘plot_oxford_grid()’ now features an option to (dis)able the coloring of orthologs depending on if they occur on significant linkage groups or not. By default, when setting a color_by argument, the orthologs that are located on non-significant linkage groups are displayed in grey. It is possible to disable this behavior by calling the function with setting argument shade_non_significant to TRUE.

Bug fixes :

• Corrected a bug that occurred when loading bed files with more than 3 fields in ‘load_orthologs()’. This function now handles bed files that have fields after the 4th column (seqName).

• Corrected a bug that happened when trying to set a custom color palette through the color_palette argument in ‘plot_oxford_grid()’. It is now possible to set a custom color palette as a list of color names.

Enhancements :

• Added a NEWS.md file to track changes to the package.
  
• Added documentation about how to customize the plots

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.