#' @title Plot retrotransposon age distributions for predictions of different genome assembly versions
#' @description Compare the abundance of retrotransposon predictions between different genome assembly versions. This way a genome assembly version bias can be either ruled out
#' or considered for subsequent conclusions.
#' @param data prediction files returned by \code{\link[LTRpred]{LTRpred}}. Usually a combined prediction file that was generated with \code{\link{combinePreds}}.
#' @param quality.filter shall false positives be filtered out as much as possible or not.
#' @param text.size size of x-axis, y-axis, and title text.
#' @param xlab x-axis label.
#' @param ylab y-axis label.
#' @param main.text title text.
#' @param y.ticks number of ticks that shall be drawn on the y-axis.
#' @param sim If \code{quality.filter = TRUE}: LTR similarity threshold. Only putative LTR transposons that fulfill this
#' LTR similarity threshold will be retained.
#' @param n.orfs If \code{quality.filter = TRUE}: minimum number of ORFs detected in the putative LTR transposon.
#' @author Hajk-Georg Drost
#' @export
gridPlotAssemblyVersions <-
function(data,
quality.filter = FALSE,
text.size = 18,
xlab = "LTR similarity",
ylab = "LTR retrotransposon count",
main.text = "",
y.ticks = 6,
sim = 70,
n.orfs = 0) {
similarity <- NULL
p <-
ggplot2::ggplot(data, ggplot2::aes(
x = factor(similarity, levels = unique(as.character(
cut(
seq(70, 100, 1),
rev(seq(100, 70,-2)),
include.lowest = TRUE,
right = TRUE
)
))),
fill = factor(similarity, levels = unique(as.character(
cut(
seq(70, 100, 1),
rev(seq(100, 70,-2)),
include.lowest = TRUE,
right = TRUE
)
)))
)) +
ggplot2::geom_bar(stat = "count") +
ggplot2::facet_grid(. ~ factor(species)) +
ggplot2::scale_fill_discrete(name = "similarity") +
ggplot2::theme_minimal() +
ggplot2::labs(x = xlab,
y = ylab,
title = main.text) +
ggplot2::theme(legend.text = ggplot2::element_text(size = text.size)) +
ggplot2::theme(
axis.title = ggplot2::element_text(size = text.size, face = "bold"),
axis.text.y = ggplot2::element_text(size = text.size, face = "bold"),
axis.text.x = ggplot2::element_text(size = text.size, face = "bold"),
strip.text.x = ggplot2::element_text(size = 14, face = "bold"),
panel.background = ggplot2::element_blank(),
plot.title = ggplot2::element_text(
size = text.size,
colour = "black",
face = "bold"
)
) +
ggplot2::theme(axis.text.x = ggplot2::element_text(
angle = 90,
vjust = 1,
hjust = 1
)) +
ggplot2::scale_fill_manual(values = customColors(length(unique(
cut(
seq(70, 100, 1),
rev(seq(100, 70,-2)),
include.lowest = TRUE,
right = TRUE
)
))), name = "Similarity") +
ggplot2::scale_y_continuous(breaks = scales::pretty_breaks(n = y.ticks))
return(p)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.