Movatterモバイル変換

macrosyntR 0.3.3

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

Redundant chromosome names from one species to another are nowaccepted
load_orthologs now handles more than two species. It uses theargument ‘bedfiles’ instead of sp1_bed and sp2_bed which are stillworking when used together.

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

created the function get_syntenic_genes(). It takes anorthologs_df as input and outputs a table with the details of alldetected blocks of two or more consecutive genes.
created the function reverse_species_order(). It takes anorthologs_df as input and outputs it with sp1 changed in sp2 and theother 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.Chrreordered, and doesn’t change the order of sp1.Chr compared with theinput data. It can be also be called in plot_oxford_grid().
‘plot_oxford_grid()’ now features an option to (dis)able thecoloring of orthologs depending on if they occur on significant linkagegroups or not. By default, when setting a color_by argument, theorthologs that are located on non-significant linkage groups aredisplayed in grey. It is possible to disable this behavior by callingthe function with setting argumentshade_non_significant toTRUE.

Corrected a bug that occurred when loading bed files with morethan 3 fields in ‘load_orthologs()’. This function now handles bed filesthat have fields after the 4th column (seqName).
Corrected a bug that happened when trying to set a custom colorpalette through the color_palette argument in ‘plot_oxford_grid()’. Itis now possible to set a custom color palette as a list of colornames.