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.
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.
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.
NEWS.md file to track changes to the
package.
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