R/plot_diverse_homology_thresholds_core_orthologs.R
In HajkD/orthologr: Comparative Genomics with R
Defines functions
plot_diverse_homology_thresholds_core_orthologs
Documented in
plot_diverse_homology_thresholds_core_orthologs
#' @title Diverse line plots visualizing the number of core 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 core orthologs
#' 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 type type of core orthologs that shall be visualized:
#' \itemize{
#' \item \code{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)
#' \item \code{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)
#' }
#' @param xlab x-axis label.
#' @param ylab y-axis label.
#' @param title plot title.
#' @author Hajk-Georg Drost
#' @export
plot_diverse_homology_thresholds_core_orthologs <-
function(ortho_tables,
species_order,
type = "both",
xlab = "Parameter set for selecting core orthologs",
ylab = "Number of corresponding core orthologs",
title = "") {
if (!is.element(type, c("gene_locus", "both")))
stop(
"Please provide a valid 'type' argument: type = 'gene_locus' or type = 'both'.",
call. = FALSE
)
qcovhsp <- perc_identity <- scope <- NULL
core_sets_multi <-
dplyr::bind_rows(
list(
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 30,
scope >= 0.5
),
"qcovhsp_50_perc_identity_30",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 30,
scope >= 0.7
),
"qcovhsp_70_perc_identity_30",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 50,
scope >= 0.5
),
"qcovhsp_50_perc_identity_50",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 50,
scope >= 0.7
),
"qcovhsp_70_perc_identity_50",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 70,
scope >= 0.7
),
"qcovhsp_70_perc_identity_70",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 70,
scope >= 0.9
),
"qcovhsp_90_perc_identity_70",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 90,
scope >= 0.9
),
"qcovhsp_90_perc_identity_90",
species_order = species_order
)
)
)
core_sets_multi$parameter <- factor(
core_sets_multi$parameter,
levels = c(
"qcovhsp_50_perc_identity_30",
"qcovhsp_70_perc_identity_30",
"qcovhsp_50_perc_identity_50",
"qcovhsp_70_perc_identity_50",
"qcovhsp_70_perc_identity_70",
"qcovhsp_90_perc_identity_70",
"qcovhsp_90_perc_identity_90"
)
)
parameter <- n_core_genes <- NULL
p_core_sets_multi <- ggplot2::ggplot(core_sets_multi,
ggplot2::aes(
x = parameter,
y = n_core_genes,
group = 1
)) + ggplot2::geom_line(size = 2) + ggplot2::geom_point(size = 4) + ggplot2::geom_text(
ggplot2::aes(label = n_core_genes),
hjust = 0,
vjust = -1.5,
size = 6
) + ggplot2::scale_y_continuous(limits = c(0, max(core_sets_multi$n_core_genes) + (
max(core_sets_multi$n_core_genes) / 10
)),
breaks = scales::pretty_breaks(n = 10)) +
ggplot2::theme_minimal() +
ggplot2::labs(x = xlab,
y = ylab,
title = title) +
ggplot2::theme(
title = ggplot2::element_text(size = 18, face = "bold"),
legend.title = ggplot2::element_text(size = 18, face = "bold"),
legend.text = ggplot2::element_text(size = 18, face = "bold"),
axis.title = ggplot2::element_text(size = 18, face = "bold"),
axis.text.y = ggplot2::element_text(size = 18, face = "bold"),
axis.text.x = ggplot2::element_text(size = 18, face = "bold"),
panel.background = ggplot2::element_blank(),
strip.text.x = ggplot2::element_text(
size = 18,
colour = "black",
face = "bold"
)
) +
ggplot2::theme(axis.text.x = ggplot2::element_text(
angle = 90,
vjust = 1,
hjust = 1
))
core_sets_multsplice_variant <-
dplyr::bind_rows(
list(
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 30,
scope >= 0.5
),
"qcovhsp_50_perc_identity_30",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 30,
scope >= 0.7
),
"qcovhsp_70_perc_identity_30",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 50,
scope >= 0.5
),
"qcovhsp_50_perc_identity_50",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 50,
scope >= 0.7
),
"qcovhsp_70_perc_identity_50",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 70,
scope >= 0.7
),
"qcovhsp_70_perc_identity_70",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 70,
scope >= 0.9
),
"qcovhsp_90_perc_identity_70",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 90,
scope >= 0.9
),
"qcovhsp_90_perc_identity_90",
species_order = species_order,
n_core_species = length(species_order)
)
)
)
core_sets_multsplice_variant$parameter <- factor(
core_sets_multsplice_variant$parameter,
levels = c(
"qcovhsp_50_perc_identity_30",
"qcovhsp_70_perc_identity_30",
"qcovhsp_50_perc_identity_50",
"qcovhsp_70_perc_identity_50",
"qcovhsp_70_perc_identity_70",
"qcovhsp_90_perc_identity_70",
"qcovhsp_90_perc_identity_90"
)
)
p_core_sets_multsplice_variant <-
p_core_sets_multi + ggplot2::geom_line(size = 2,
data = core_sets_multsplice_variant,
colour = "#008B45FF") + ggplot2::geom_point(size = 4,
data = core_sets_multsplice_variant,
colour = "#008B45FF") + ggplot2::geom_text(
ggplot2::aes(label = n_core_genes),
data = core_sets_multsplice_variant,
colour = "#008B45FF",
hjust = 0,
vjust = 3,
size = 6
)
if (type == "gene_locus")
return(p_core_sets_multi)
if (type == "both")
return(p_core_sets_multsplice_variant)
}
HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.
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Defines functions plot_diverse_homology_thresholds_core_orthologs
Documented in plot_diverse_homology_thresholds_core_orthologs
#' @title Diverse line plots visualizing the number of core 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 core orthologs
#' 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 type type of core orthologs that shall be visualized:
#' \itemize{
#' \item \code{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)
#' \item \code{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)
#' }
#' @param xlab x-axis label.
#' @param ylab y-axis label.
#' @param title plot title.
#' @author Hajk-Georg Drost
#' @export
plot_diverse_homology_thresholds_core_orthologs <-
function(ortho_tables,
species_order,
type = "both",
xlab = "Parameter set for selecting core orthologs",
ylab = "Number of corresponding core orthologs",
title = "") {
if (!is.element(type, c("gene_locus", "both")))
stop(
"Please provide a valid 'type' argument: type = 'gene_locus' or type = 'both'.",
call. = FALSE
)
qcovhsp <- perc_identity <- scope <- NULL
core_sets_multi <-
dplyr::bind_rows(
list(
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 30,
scope >= 0.5
),
"qcovhsp_50_perc_identity_30",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 30,
scope >= 0.7
),
"qcovhsp_70_perc_identity_30",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 50,
scope >= 0.5
),
"qcovhsp_50_perc_identity_50",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 50,
scope >= 0.7
),
"qcovhsp_70_perc_identity_50",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 70,
scope >= 0.7
),
"qcovhsp_70_perc_identity_70",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 70,
scope >= 0.9
),
"qcovhsp_90_perc_identity_70",
species_order = species_order
),
testCoreOrthoParamsGeneLocus(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 90,
scope >= 0.9
),
"qcovhsp_90_perc_identity_90",
species_order = species_order
)
)
)
core_sets_multi$parameter <- factor(
core_sets_multi$parameter,
levels = c(
"qcovhsp_50_perc_identity_30",
"qcovhsp_70_perc_identity_30",
"qcovhsp_50_perc_identity_50",
"qcovhsp_70_perc_identity_50",
"qcovhsp_70_perc_identity_70",
"qcovhsp_90_perc_identity_70",
"qcovhsp_90_perc_identity_90"
)
)
parameter <- n_core_genes <- NULL
p_core_sets_multi <- ggplot2::ggplot(core_sets_multi,
ggplot2::aes(
x = parameter,
y = n_core_genes,
group = 1
)) + ggplot2::geom_line(size = 2) + ggplot2::geom_point(size = 4) + ggplot2::geom_text(
ggplot2::aes(label = n_core_genes),
hjust = 0,
vjust = -1.5,
size = 6
) + ggplot2::scale_y_continuous(limits = c(0, max(core_sets_multi$n_core_genes) + (
max(core_sets_multi$n_core_genes) / 10
)),
breaks = scales::pretty_breaks(n = 10)) +
ggplot2::theme_minimal() +
ggplot2::labs(x = xlab,
y = ylab,
title = title) +
ggplot2::theme(
title = ggplot2::element_text(size = 18, face = "bold"),
legend.title = ggplot2::element_text(size = 18, face = "bold"),
legend.text = ggplot2::element_text(size = 18, face = "bold"),
axis.title = ggplot2::element_text(size = 18, face = "bold"),
axis.text.y = ggplot2::element_text(size = 18, face = "bold"),
axis.text.x = ggplot2::element_text(size = 18, face = "bold"),
panel.background = ggplot2::element_blank(),
strip.text.x = ggplot2::element_text(
size = 18,
colour = "black",
face = "bold"
)
) +
ggplot2::theme(axis.text.x = ggplot2::element_text(
angle = 90,
vjust = 1,
hjust = 1
))
core_sets_multsplice_variant <-
dplyr::bind_rows(
list(
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 30,
scope >= 0.5
),
"qcovhsp_50_perc_identity_30",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 30,
scope >= 0.7
),
"qcovhsp_70_perc_identity_30",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 50,
perc_identity >= 50,
scope >= 0.5
),
"qcovhsp_50_perc_identity_50",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 50,
scope >= 0.7
),
"qcovhsp_70_perc_identity_50",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 70,
perc_identity >= 70,
scope >= 0.7
),
"qcovhsp_70_perc_identity_70",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 70,
scope >= 0.9
),
"qcovhsp_90_perc_identity_70",
species_order = species_order,
n_core_species = length(species_order)
),
testCoreOrthoParamsSpliceVariant(
dplyr::filter(
ortho_tables,
qcovhsp >= 90,
perc_identity >= 90,
scope >= 0.9
),
"qcovhsp_90_perc_identity_90",
species_order = species_order,
n_core_species = length(species_order)
)
)
)
core_sets_multsplice_variant$parameter <- factor(
core_sets_multsplice_variant$parameter,
levels = c(
"qcovhsp_50_perc_identity_30",
"qcovhsp_70_perc_identity_30",
"qcovhsp_50_perc_identity_50",
"qcovhsp_70_perc_identity_50",
"qcovhsp_70_perc_identity_70",
"qcovhsp_90_perc_identity_70",
"qcovhsp_90_perc_identity_90"
)
)
p_core_sets_multsplice_variant <-
p_core_sets_multi + ggplot2::geom_line(size = 2,
data = core_sets_multsplice_variant,
colour = "#008B45FF") + ggplot2::geom_point(size = 4,
data = core_sets_multsplice_variant,
colour = "#008B45FF") + ggplot2::geom_text(
ggplot2::aes(label = n_core_genes),
data = core_sets_multsplice_variant,
colour = "#008B45FF",
hjust = 0,
vjust = 3,
size = 6
)
if (type == "gene_locus")
return(p_core_sets_multi)
if (type == "both")
return(p_core_sets_multsplice_variant)
}
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