#' Boxplots of cell density.
#'
#' \code{figure_cell_density()} reproduces the compound figure of the cell
#' denisty data in section x.xx of Benjamin Gordon's PhD thesis.
#'
#' \code{figure_cell_density()} summarises the cell density data located in
#' \code{./data-raw} The figure can be saved to \code{./figs/} if required.
#'
#' @param view.plot Logical indicating if the plot should be printed to the plot
#' viewer.
#' @param save.plot Logical indicating if the plot should be saved to
#' \code{./figs/}.
#' @param plot.name Name of plot.
#'
#' @note Although this function is exported, \code{figure_cell_density()}
#' was not intended to be used outside of this package.
#'
#' @seealso
#' \code{\link[ggplot2]{ggplot}}
#'
#' @author Benjamin R. Gordon
#'
#' @export
#'
figure_cell_density <- function(view.plot = TRUE,
save.plot = FALSE,
plot.name = "cell_density_plot") {
# load data and modify
celldens <- readr::read_csv("./data-raw/cell-densities.csv")
colnames(celldens)[3] <- "density"
celldens$class <- factor(celldens$class,
levels = c("control", "eCO2", "eT", "eCO2eT"))
celldens$day <- factor(c(rep("day 5", 24),
rep("day 10", 24),
rep("day 14", 24)),
levels = c("day 5", "day 10", "day 14")
)
# plot
cell_plot <-
ggplot(celldens, aes(x = class, y = density)) +
geom_boxplot() +
facet_grid(.~day) +
xlab("Treatment") +
ylab("Cell density") +
theme(strip.background = element_blank(),
strip.text = element_text(size = 14),
axis.text = element_text(size = 12, colour = "grey65"),
axis.title = element_text(size = 14),
axis.ticks = element_blank()
)
ggsave("./cell-density-boxplot.pdf",
height = 5, width = 10, units = "in")
grDevices::graphics.off()
# Create, view, save plot ----------------------------------------------------
if (view.plot) {
print(cell_plot)
}
if (save.plot) {
grDevices::pdf(paste(c("./figs/", plot.name, ".pdf"), collapse = ""),
width = 10,
height = 5,
useDingbats = FALSE)
cell_plot
grDevices::dev.off()
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.