Given a ortho table generated with generate_ortholog_tables_all, this function will visualize the number of core orthologs using a diverse range of homology thresholds to enable an analytical decision for chosing homology thresholds to define orthologous genes.

plot_diverse_homology_thresholds_core_orthologs(
  ortho_tables,
  species_order,
  type = "both",
  xlab = "Parameter set for selecting core orthologs",
  ylab = "Number of corresponding core orthologs",
  title = ""
)

Arguments

ortho_tables

a ortho tables that was generated with generate_ortholog_tables_all.

species_order

a character string specifying species names listed in the order of phylogenetic/taxonomic distance from the query species. The species names must match with the species names present in the ortho_tables.

type

type of core orthologs that shall be visualized:

  • type = "gene_locus": visualizes the number of core orthologs for a gene locus (hence, different splice variants can represent the same orthologous gene locus relationship)

  • type = "both": visualizes the difference in numbers of core orthologs for a gene locus versus orthologous splice variant (thus, only the same splice variant can represent the same orthologous gene locus relationship)

xlab

x-axis label.

ylab

y-axis label.

title

plot title.

Author

Hajk-Georg Drost