#' Plot of Photosynthetic Yield (FvFm).
#'
#' \code{figure_fvfm()} produces the photosynthetic yield plot in section 4 of
#' Benjamin Gordon's PhD thesis.
#'
#' \code{figure_fvfm()} plots the PAM data located in \code{./data}.
#' The figure can be saved to \code{./figs/} if required.
#'
#' @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_fvfm()}
#' was not intended to be used outside of this package.
#'
#' @seealso
#' \code{\link[ggplot2]{ggplot}}
#'
#' @author Benjamin R. Gordon
#'
#' @export
#'
figure_fvfm <- function(save.plot = FALSE,
plot.name = "fvfm_plot") {
# plot
fvfm_plot <- ggplot(pamdata, aes(x = day,
y = FvFm,
colour = class,
shape = class,
fill = class)) +
geom_point(size = 3, show.legend = TRUE) +
geom_path() +
scale_x_continuous(name = "Time (days)",
labels = c(1:13),
breaks = c(1:13)) +
scale_y_continuous(name = expression(Quantum~Yield~PSII~(F[v]/F[m]))) +
scale_colour_manual(values = phdhelpr::qual_colours[c(3, 2, 1, 6)],
name = NULL,
labels = c("control", expression(eCO[2]), "eT",
expression(eCO[2]*eT))) +
scale_shape_manual(values = c(21:24),
name = NULL,
labels = c("control", expression(eCO[2]), "eT",
expression(eCO[2]*eT))) +
scale_fill_manual(values = grDevices::adjustcolor(phdhelpr::qual_colours[c(3, 2, 1, 6)],
alpha.f = 0.5),
name = NULL,
labels = c("control", expression(eCO[2]), "eT",
expression(eCO[2]*eT))) +
theme(panel.background = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.major.y = element_line(colour = "grey90",
size = 0.6),
axis.text = element_text(size = 10, colour = "grey65"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(),
legend.key = element_blank(),
legend.text = element_text(size = 14),
legend.text.align = 0
)
# View or save plot ----------------------------------------------------------
if (save.plot) {
grDevices::pdf(paste(c("./figs/", plot.name, ".pdf"), collapse = ""),
width = 10,
height = 5,
useDingbats = FALSE)
fvfm_plot
grDevices::dev.off()
}
fvfm_plot
}
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