Diverse line plots visualizing the number of pairwise orthologs within a ortho table generated with generate_ortholog_tables_all based on different sets of homology thresholds.

Given a ortho table generated with generate_ortholog_tables_all, this function will visualize the number of pairwise orthologs inferred between a reference species A vs a set of subject species B_1, B_2, ...,B_N using a diverse range of homology thresholds to enable an analytical decision for chosing homology thresholds to define orthologous genes.

plot_diverse_homology_thresholds(
  ortho_tables,
  species_order,
  xlab = "Subject Species",
  ylab = "Number of reciprocal best hit 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.

xlab

x-axis label.

ylab

y-axis label.

title

plot title.

Author

Hajk-Georg Drost