R/plot_diverse_homology_thresholds.R
In HajkD/orthologr: Comparative Genomics with R
Defines functions
plot_diverse_homology_thresholds
Documented in
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.
#' @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.
#' @param ortho_tables a \code{ortho tables} that was generated with \code{\link{generate_ortholog_tables_all}}.
#' @param 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}.
#' @param xlab x-axis label.
#' @param ylab y-axis label.
#' @param title plot title.
#' @author Hajk-Georg Drost
#' @export
plot_diverse_homology_thresholds <-
function(ortho_tables,
species_order,
xlab = "Subject Species",
ylab = "Number of reciprocal best hit orthologs",
title = "") {
qcovhsp <-
scope <- perc_identity <- subject_species <- n_orthologs <- NULL
qcovhsp_70_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_70_perc_identity_50 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 50
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_70_perc_identity_70 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 70
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_70_perc_identity_90 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 90
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_30_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 30,
scope >= 0.3,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_50_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
scope >= 0.5,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_50 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 50
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_70 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 70
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_90 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 90
),
subject_species
),
n_orthologs = dplyr::n())
p_all_ortho_thresholds <-
orthologr::plot_pairwise_orthologs(
ortho_tables = ortho_tables,
species_order = species_order,
n_core_orthologs = NULL,
xlab = xlab,
ylab = ylab,
title = title
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_30,
size = 2,
colour = "#3B4992FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_30,
colour = "#3B4992FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#3B4992FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_50,
size = 2,
colour = "#808180FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_50,
colour = "#808180FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_50,
hjust = 0,
vjust = 3,
size = 4,
colour = "#808180FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_70,
size = 2,
colour = "#EE0000FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_70,
colour = "#EE0000FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_70,
hjust = 0,
vjust = 3,
size = 4,
colour = "#EE0000FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_90,
size = 2,
colour = "#008B45FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_90,
colour = "#008B45FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_90,
hjust = 0,
vjust = 3,
size = 4,
colour = "#008B45FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_30_perc_identity_30,
size = 2,
colour = "#631879FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_30_perc_identity_30,
colour = "#631879FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_30_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#631879FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_50_perc_identity_30,
size = 2,
colour = "#008280FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_50_perc_identity_30,
colour = "#008280FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_50_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#008280FF"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_30,
size = 2,
colour = "#BB0021FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_30,
colour = "#BB0021FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#BB0021FF"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_50,
size = 2,
colour = "#5F559BFF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_50,
colour = "#5F559BFF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_50,
hjust = 0,
vjust = 3,
size = 4,
colour = "#5F559BFF"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_70,
size = 2,
colour = "darkgreen"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_70,
colour = "darkgreen") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_70,
hjust = 0,
vjust = 3,
size = 4,
colour = "darkgreen"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_90,
size = 2,
colour = "#A20056FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_90,
colour = "#A20056FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_90,
hjust = 0,
vjust = 3,
size = 4,
colour = "#A20056FF"
) + ggplot2::scale_fill_manual(
values = c(
"#3B4992FF",
"#808180FF",
"#EE0000FF",
"#008B45FF",
"#631879FF",
"#008280FF",
"#BB0021FF",
"#5F559BFF",
"darkgreen",
"#A20056FF"
),
name = "Parameter Options",
labels = c(
"qcovhsp_70_perc_identity_30",
"qcovhsp_70_perc_identity_50",
"qcovhsp_70_perc_identity_70",
"qcovhsp_70_perc_identity_90",
"qcovhsp_30_perc_identity_30",
"qcovhsp_50_perc_identity_30",
"qcovhsp_90_perc_identity_30",
"qcovhsp_90_perc_identity_50",
"qcovhsp_90_perc_identity_70",
"qcovhsp_90_perc_identity_90"
)
)
return(p_all_ortho_thresholds)
}
HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.
R Package Documentation
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Defines functions plot_diverse_homology_thresholds
Documented in 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.
#' @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.
#' @param ortho_tables a \code{ortho tables} that was generated with \code{\link{generate_ortholog_tables_all}}.
#' @param 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}.
#' @param xlab x-axis label.
#' @param ylab y-axis label.
#' @param title plot title.
#' @author Hajk-Georg Drost
#' @export
plot_diverse_homology_thresholds <-
function(ortho_tables,
species_order,
xlab = "Subject Species",
ylab = "Number of reciprocal best hit orthologs",
title = "") {
qcovhsp <-
scope <- perc_identity <- subject_species <- n_orthologs <- NULL
qcovhsp_70_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_70_perc_identity_50 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 50
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_70_perc_identity_70 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 70
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_70_perc_identity_90 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
scope >= 0.7,
perc_identity >= 90
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_30_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 30,
scope >= 0.3,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_50_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
scope >= 0.5,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_30 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 30
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_50 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 50
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_70 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 70
),
subject_species
),
n_orthologs = dplyr::n())
qcovhsp_90_perc_identity_90 <-
dplyr::summarize(dplyr::group_by(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
scope >= 0.9,
perc_identity >= 90
),
subject_species
),
n_orthologs = dplyr::n())
p_all_ortho_thresholds <-
orthologr::plot_pairwise_orthologs(
ortho_tables = ortho_tables,
species_order = species_order,
n_core_orthologs = NULL,
xlab = xlab,
ylab = ylab,
title = title
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_30,
size = 2,
colour = "#3B4992FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_30,
colour = "#3B4992FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#3B4992FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_50,
size = 2,
colour = "#808180FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_50,
colour = "#808180FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_50,
hjust = 0,
vjust = 3,
size = 4,
colour = "#808180FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_70,
size = 2,
colour = "#EE0000FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_70,
colour = "#EE0000FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_70,
hjust = 0,
vjust = 3,
size = 4,
colour = "#EE0000FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_70_perc_identity_90,
size = 2,
colour = "#008B45FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_70_perc_identity_90,
colour = "#008B45FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_70_perc_identity_90,
hjust = 0,
vjust = 3,
size = 4,
colour = "#008B45FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_30_perc_identity_30,
size = 2,
colour = "#631879FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_30_perc_identity_30,
colour = "#631879FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_30_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#631879FF"
) + ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_50_perc_identity_30,
size = 2,
colour = "#008280FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_50_perc_identity_30,
colour = "#008280FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_50_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#008280FF"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_30,
size = 2,
colour = "#BB0021FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_30,
colour = "#BB0021FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_30,
hjust = 0,
vjust = 3,
size = 4,
colour = "#BB0021FF"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_50,
size = 2,
colour = "#5F559BFF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_50,
colour = "#5F559BFF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_50,
hjust = 0,
vjust = 3,
size = 4,
colour = "#5F559BFF"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_70,
size = 2,
colour = "darkgreen"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_70,
colour = "darkgreen") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_70,
hjust = 0,
vjust = 3,
size = 4,
colour = "darkgreen"
) +
ggplot2::geom_line(
ggplot2::aes(
x = subject_species,
y = n_orthologs,
group = 1
),
data = qcovhsp_90_perc_identity_90,
size = 2,
colour = "#A20056FF"
) + ggplot2::geom_point(size = 4,
data = qcovhsp_90_perc_identity_90,
colour = "#A20056FF") +
ggplot2::geom_text(
ggplot2::aes(label = n_orthologs),
data = qcovhsp_90_perc_identity_90,
hjust = 0,
vjust = 3,
size = 4,
colour = "#A20056FF"
) + ggplot2::scale_fill_manual(
values = c(
"#3B4992FF",
"#808180FF",
"#EE0000FF",
"#008B45FF",
"#631879FF",
"#008280FF",
"#BB0021FF",
"#5F559BFF",
"darkgreen",
"#A20056FF"
),
name = "Parameter Options",
labels = c(
"qcovhsp_70_perc_identity_30",
"qcovhsp_70_perc_identity_50",
"qcovhsp_70_perc_identity_70",
"qcovhsp_70_perc_identity_90",
"qcovhsp_30_perc_identity_30",
"qcovhsp_50_perc_identity_30",
"qcovhsp_90_perc_identity_30",
"qcovhsp_90_perc_identity_50",
"qcovhsp_90_perc_identity_70",
"qcovhsp_90_perc_identity_90"
)
)
return(p_all_ortho_thresholds)
}
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