/
gg_species_promotor_dist_blast_tbl.R
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gg_species_promotor_dist_blast_tbl.R
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#' @title Plot pairwise promotor sequence distance distributions of orthologous genes
#' @description This function enables users to plot pairwise promotor sequence distance distributions of orthologous genes.
#' @param blast_tbl a \code{blast_tbl}.
#' @param type type of sustitution rate quantification that shall be visualized on the y-axis. Options are:
#' \itemize{
#' \item \code{type = "promotor_dist"}
#' \item \code{type = "promotor_aln_score"}
#' \item \code{type = "promotor_indel_blocks"}
#' \item \code{type = "promotor_indels"}
#' }
#' @param order a character vector specifying the order of the species using their scientific names (which have to match the species names stored in the \code{subject_species}
#' column of the input \code{blast_tbl}).
#' @param xlab label of x-axis.
#' @param ylab label of y-axis.
#' @param title title label.
#' @author Hajk-Georg Drost
#' @export
gg_species_promotor_dist_blast_tbl <- function(blast_tbl, type, order, xlab = "", ylab = "", title = "") {
if (!is.element(type, c("promotor_dist", "promotor_aln_score", "promotor_indel_blocks", "promotor_indels")))
stop("Please specify a type that is supported by this function.", call. = FALSE)
subject_species <- promotor_dist <- promotor_aln_score <- promotor_indel_blocks <- promotor_indels <- ..density.. <- NULL
if (type == "promotor_dist") {
p <-
ggplot2::ggplot(
blast_tbl,
ggplot2::aes(
x = promotor_dist,
y = factor(subject_species, levels = rev(order)),
fill = subject_species,
colour = subject_species,
height = ..density..
)
)
}
if (type == "promotor_aln_score") {
p <-
ggplot2::ggplot(
blast_tbl,
ggplot2::aes(
x = promotor_aln_score,
y = factor(subject_species, levels = rev(order)),
fill = subject_species,
colour = subject_species,
height = ..density..
)
)
}
if (type == "promotor_indel_blocks") {
p <-
ggplot2::ggplot(
blast_tbl,
ggplot2::aes(
x = promotor_indel_blocks,
y = factor(subject_species, levels = rev(order)),
fill = subject_species,
colour = subject_species,
height = ..density..
)
)
}
if (type == "promotor_indels") {
p <-
ggplot2::ggplot(
blast_tbl,
ggplot2::aes(
x = promotor_indels,
y = factor(subject_species, levels = rev(order)),
fill = subject_species,
colour = subject_species,
height = ..density..
)
)
}
p <- p +
ggridges::geom_density_ridges(
scale = 5,
show.legend = FALSE,
alpha = 0.4,
size = 1.5,
stat = "density", trim = TRUE
) + ggridges::theme_ridges() + ggsci::scale_colour_lancet() + ggsci::scale_fill_lancet() + ggplot2::labs(x = xlab,
y = ylab) +
ggplot2::theme(legend.text = ggplot2::element_text(size = 18)) +
ggplot2::theme(
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(),
plot.title = ggplot2::element_text(
size = 18,
colour = "black",
face = "bold"
)
) + ggplot2::ggtitle(title) + ggplot2::scale_x_continuous(breaks = scales::pretty_breaks(n = 8))
return(p)
}