NEWS.md

In macrosyntR: Draw Ordered Oxford Grids and Chord Diagrams

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

macrosyntR documentation built on Nov. 14, 2023, 5:09 p.m.