generate_ortholog_tables_all
based on different sets of homology thresholds.R/plot_diverse_homology_thresholds_core_orthologs.R
plot_diverse_homology_thresholds_core_orthologs.RdGiven 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 = ""
)a ortho tables that was generated with generate_ortholog_tables_all.
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 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)
x-axis label.
y-axis label.
plot title.