-
Notifications
You must be signed in to change notification settings - Fork 27
/
plot_diverse_homology_thresholds.Rd
35 lines (31 loc) · 1.38 KB
/
plot_diverse_homology_thresholds.Rd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot_diverse_homology_thresholds.R
\name{plot_diverse_homology_thresholds}
\alias{plot_diverse_homology_thresholds}
\title{Diverse line plots visualizing the number of pairwise orthologs within a ortho table generated with \code{\link{generate_ortholog_tables_all}}
based on different sets of homology thresholds.}
\usage{
plot_diverse_homology_thresholds(
ortho_tables,
species_order,
xlab = "Subject Species",
ylab = "Number of reciprocal best hit orthologs",
title = ""
)
}
\arguments{
\item{ortho_tables}{a \code{ortho tables} that was generated with \code{\link{generate_ortholog_tables_all}}.}
\item{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 \code{ortho_tables}.}
\item{xlab}{x-axis label.}
\item{ylab}{y-axis label.}
\item{title}{plot title.}
}
\description{
Given a ortho table generated with \code{\link{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.
}
\author{
Hajk-Georg Drost
}