R/graphics.R
In BEE-Univ-Grenoble/BeePODYNA:
Defines functions
plot.population
plot.community
com_plot
Documented in
com_plot
plot.community
plot.population
#' @import graphics
#' @import grDevices
NULL
#' plot_population
#'
#' plot one given population and its capacity line.
#'
#' @param x a population object
#' @param ... every argument for the \code{\link[graphics]{plot}} function such as graphical parameters for lines.
#' Classical \code{\link[graphics]{graphical parameter}} applies on the population curve, NOT on the capacity line (custom parameter need to be given, as exemple capacity_lty).
#' \itemize{
#' \item \strong{type} for the size line, set to \code{'b'} by default.
#' \item \strong{xlab} set to \code{'Time'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{ylab} set to \code{'Size'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{main} set to use the pop label by default, see \code{\link[graphics]{title}}.
#' }
#' @param capacity_line set to \code{TRUE} by default, if a dashed line must be drawned to show the capacity.
#' @param capacity_lty set to \code{3} by default.
#' @param text_print set to \code{TRUE} by default, whether there is a text on the capacipty line or not (writting population 'K label' by default).
#' @param add set to \code{FALSE} by default, to add another population plot on a precedent one.
#'
#'
#' @seealso
#' \itemize{
#' \item \code{\link[graphics]{plot}}, \code{\link[graphics]{title}} and \code{\link[graphics]{par}} for plot parameter that were omitted on this documentation
#' \item \code{\link[BeePODYNA]{population}} for every aspect about population and community creations.
#' }
#'
#' @examples
#' data(hudson)
#' hare <- hudson$hare
#' lynx <- hudson$lynx
#'
#' plot(hare,
#' col = "red", pch = 15, type = "b", capacity_lty = 3,
#' lty = 2, main = "Hudson data"
#' )
#'
#' plot(lynx,
#' col = "blue", pch = 15, type = "b", capacity_lty = 3,
#' add = TRUE, lty = 1, capacity_line = TRUE
#' )
#' @author Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>
#'
#' @export
plot.population <- function(x,
...,
capacity_line = TRUE,
capacity_lty = 3,
text_print = TRUE,
add = FALSE) {
delta_x <- (max(x$time) - min(x$time)) * 0.1
delta_y <- (max(x$size) - min(x$size)) * 0.2
default_par <- list(
col = 1,
type = "b",
xlab = "Time",
ylab = "Population size",
main = x$label,
xlim = c(min(x$time) - delta_x, max(x$time) + delta_x),
ylim = c(min(x$size) - delta_y, max(x$size) + delta_y)
)
call_par <- list(...)
names_defaut_par <- names(default_par)
for (i in seq_along(default_par)) {
if (!names_defaut_par[i] %in% names(call_par) | is.null(call_par[[names_defaut_par[i]]])) {
call_par[[names_defaut_par[i]]] <- default_par[[names_defaut_par[i]]]
}
}
if ("log" %in% names(call_par)) {
call_par$log <- sub("x", "", call_par$log)
if (regexec("y", call_par$log)[[1]] > 0) {
if (default_par$ylim[1] < 0) call_par$ylim[1] <- 1
}
}
if (!add) {
empty_par <- c(list(x = 1, y = 1), call_par)
empty_par$type <- "n"
do.call(plot, empty_par)
}
line_par <- c(list(x = x$time, y = x$size), call_par)
line_par$xlim <- NULL
line_par$xlim <- NULL
line_par$ylim <- NULL
line_par$xlab <- NULL
line_par$ylab <- NULL
line_par$main <- NULL
line_par$log <- NULL
do.call(lines, line_par)
if (capacity_line) {
abline(h = x$capacity, lty = capacity_lty, col = call_par$col)
}
if (text_print) {
text(
x = x$time[1], y = x$capacity,
paste("K", x$label, sep = " "),
pos = 3,
col = call_par$col
)
}
}
#' plot.community
#'
#' plot one given community and its capacity line.
#'
#' @param x a community object
#' @param ... every argument for the \code{\link[graphics]{plot}} function such as graphical parameters for lines.
#' Classical \code{\link[graphics]{graphical parameter}} applies on the population curve, NOT on the capacity line (custom parameter need to be given, as exemple capacity_lty).
#' \itemize{
#' \item \strong{type} for the size line, set to \code{'b'} by default.
#' \item \strong{xlab} set to \code{'Time'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{ylab} set to \code{'Size'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{main} set to use the pop label by default, see \code{\link[graphics]{title}}.
#' }
#' @param capacity_line set to \code{TRUE} by default, if a dashed line must be drawned to show the capacity.
#' @param capacity_lty set to \code{3} by default.
#' @param text_print set to \code{TRUE} by default, whether there is a text on the capacipty line or not (writting population 'K label' by default).
#' @param add set to \code{FALSE} by default, to add another population plot on a precedent one.
#'
#' @note For \strong{capacity_line}, \strong{capacity_lty}, \strong{type}, \strong{text_print} and \strong{text_x} parameters, values can be a single value or a vector of value. If the vector length is inferior to the population number in the community, the value or the vector will be copy.
#'
#' @seealso
#' \itemize{
#' \item \code{\link[graphics]{plot}}, \code{\link[graphics]{title}} and \code{\link[graphics]{par}} for plot parameter that were omitted on this documentation
#' \item \code{\link[BeePODYNA]{plot.population}}, \code{\link[BeePODYNA]{population}}, \code{\link[BeePODYNA]{community}} for every aspect about population and community creations.
#' }
#'
#' @import graphics
#'
#' @examples
#' data(hudson)
#' plot(hudson)
#' @author Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>
#'
#' @export
plot.community <- function(x, ...,
capacity_line = TRUE,
capacity_lty = 3,
text_print = TRUE,
add = FALSE) {
n_pop <- length(x)
capacity_line <- rep(capacity_line, n_pop)
capacity_lty <- rep(capacity_lty, n_pop)
text_print <- rep(text_print, n_pop)
com_time <- unlist(sapply(x$populations, "[[", 3))
delta_x <- (max(com_time) - min(com_time))
if(delta_x == 0) delta_x <- 0.1 else delta_x <- delta_x * 0.1
com_size <- unlist(sapply(x$populations, "[[", 2))
delta_y <- (max(com_size) - min(com_size)) * 0.1
if(delta_y == 0) delta_y <- 0.1 else delta_y <- delta_y * 0.1
default_par <- list(
col = rep(1, n_pop),
type = rep("b", n_pop),
xlab = "Time",
ylab = "Population size",
main = x$label,
xlim = c(min(com_time) - delta_x, max(com_time) + delta_x),
ylim = c(min(com_size) - delta_y, max(com_size) + delta_y)
)
call_par <- list(...)
names_defaut_par <- names(default_par)
for (i in seq_along(default_par)) {
if (!names_defaut_par[i] %in% names(call_par) | is.null(call_par[[names_defaut_par[i]]])) {
call_par[[names_defaut_par[i]]] <- default_par[[names_defaut_par[i]]]
}
}
for (i in seq_along(call_par)) {
if(length(call_par[[i]]) < n_pop) call_par[[i]] <- rep(call_par[[i]], n_pop)
}
if ("log" %in% names(call_par)) {
call_par$log <- paste(sub("x", "", call_par$log), collapse = "")
if (regexec("y", call_par$log)[[1]] > 0) {
if (default_par$ylim[1] < 0) call_par$ylim[1] <- 1
}
}
if (!add) {
empty_par <- c(list(x = 1, y = 1), call_par)
tmpx <- empty_par$xlim[1:2]
tmpy <- empty_par$ylim[1:2]
empty_par <- lapply(empty_par, FUN = function(x) x[1])
empty_par$xlim <- tmpx
empty_par$ylim <- tmpy
empty_par$type <- "n"
do.call(plot, empty_par)
}
for (i in 1:n_pop) {
line_par <- call_par
line_par <- lapply(line_par, FUN = function(x) x[i])
line_par <- c(list(x = x$populations[[i]]$time, y = x$populations[[i]]$size), line_par)
line_par$xlim <- NULL
line_par$xlim <- NULL
line_par$ylim <- NULL
line_par$xlab <- NULL
line_par$ylab <- NULL
line_par$main <- NULL
line_par$log <- NULL
do.call(lines, line_par)
if (capacity_line[i]) {
abline(h = x$populations[[i]]$capacity, lty = capacity_lty[i], col = call_par$col[i])
}
if (text_print[i]) {
text(
x = x$populations[[i]]$time[1], y = x$populations[[i]]$capacity,
paste("K", x$populations[[i]]$label, sep = " "),
pos = 3,
col = call_par$col[i]
)
}
}
}
#' com_plot
#'
#' plot a given community of length = 2 with 2 dimmensionnal place.
#'
#' @param x a community object
#' @param ... every argument for the \code{\link[graphics]{plot}} function such as titles, labels and windows limitation.
#' Classical \code{\link[graphics]{graphical parameter}} applies on the population curve, NOT on the capacity line (custom parameter need to be given, as exemple capacity_lty).
#' \itemize{
#' \item \strong{xlab} set to \code{'Time'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{ylab} set to \code{'Size'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{main} set to use the pop label by default, see \code{\link[graphics]{title}}.
#' }
#' @param xpop the population for the x axise
#' @param ypop the population for the y axise
#' @param capacity_line set to \code{TRUE} by default, if a dashed line must be drawned to show the capacity.
#' @param capacity_lty set to \code{3} by default.
#' @param text_print set to \code{TRUE} by default, whether there is a text on the capacipty line or not (writting population 'K label' by default).
#' @param first_p the first point in the time serie to be drawn. All points are drawn by default.
#' @param white the percentage of white for the beginning of the color scale. \code{0.8} by default.
#' @param add set to \code{FALSE} by default, to add another com_plot plot on a precedent one.
#'
#' @note For \strong{capacity_line}, \strong{capacity_lty} and \strong{text_print} parameters, values can be a single value or a vector of value. If the vector length is inferior to the population number in the community, the value or the vector will be copy.
#'
#' @seealso
#' \itemize{
#' \item \code{\link[graphics]{plot}}, \code{\link[graphics]{title}} and \code{\link[graphics]{par}} for plot parameter that were omitted on this documentation
#' \item \code{\link[BeePODYNA]{plot.population}}, \code{\link[BeePODYNA]{population}}, \code{\link[BeePODYNA]{community}} for every aspect about population and community creations.
#' }
#'
#' @import graphics
#'
#' @examples
#' data(hudson)
#' com_plot(hudson)
#' @author Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>
#'
#' @export
com_plot <- function(x, ...,
xpop = 1,
ypop = 2,
capacity_line = c(TRUE, TRUE),
capacity_lty = c(3, 3),
text_print = c(TRUE, TRUE),
first_p = 1,
white = 0.8,
add = FALSE) {
n_pop <- length(x)
capacity_line <- rep(capacity_line, n_pop)
capacity_lty <- rep(capacity_lty, n_pop)
text_print <- rep(text_print, n_pop)
com_x <- x$populations[[xpop]]$size
delta_x <- (max(com_x) - min(com_x))
if (delta_x == 0) delta_x <- 0.1 else delta_x <- delta_x * 0.1
com_y <- x$populations[[ypop]]$size
delta_y <- (max(com_y) - min(com_y)) * 0.1
if (delta_y == 0) delta_y <- 0.1 else delta_y <- delta_y * 0.1
default_par <- list(
col = rep(1, n_pop),
type = rep("b", n_pop),
xlab = x$populations[[xpop]]$label,
ylab = x$populations[[ypop]]$label,
main = x$label,
xlim = c(min(com_x) - delta_x, max(com_x) + delta_x),
ylim = c(min(com_y) - delta_y, max(com_y) + delta_y)
)
call_par <- list(...)
names_defaut_par <- names(default_par)
for (i in seq_along(default_par)) {
if (!names_defaut_par[i] %in% names(call_par) | is.null(call_par[[names_defaut_par[i]]])) {
call_par[[names_defaut_par[i]]] <- default_par[[names_defaut_par[i]]]
}
}
for (i in seq_along(call_par)) {
if (length(call_par[[i]]) < n_pop) call_par[[i]] <- rep(call_par[[i]], n_pop)
}
if ("log" %in% names(call_par)) {
tmp_y <- paste(sub("x","", call_par$log), collapse = "")
if (regexec("y", tmp_y)[[1]] > 0) {
if (default_par$ylim[1] < 0) call_par$ylim[1] <- 1
}
tmp_x <- paste(sub("y","", call_par$log), collapse = "")
if (regexec("x", tmp_x)[[1]] > 0) {
if (default_par$xlim[1] < 0) call_par$xlim[1] <- 1
}
}
if (!add) {
empty_par <- c(list(x = 1, y = 1), call_par)
tmpx <- empty_par$xlim[1:2]
tmpy <- empty_par$ylim[1:2]
empty_par <- lapply(empty_par, FUN = function(x) x[1])
empty_par$xlim <- tmpx
empty_par$ylim <- tmpy
empty_par$type <- "n"
do.call(plot, empty_par)
}
com_time <- 1
x_size <- x$populations[[xpop]]$size
y_size <- x$populations[[ypop]]$size
x_time <- x$populations[[ypop]]$time
# color gradient, only gray for the moment
gray <- gray.colors(length(x_size), start = white, end = 0, gamma = 2.2)
for (i in first_p:length(x_size)) {
segments(
x0 = x_size[i], y0 = y_size[i],
x1 = x_size[i + 1], y1 = y_size[i + 1],
col = gray[i]
)
text(
x = x_size[i], y = y_size[i],
label = x_time[i], col = gray[i], pos = 3
) # modifier pour dire si on prend le time sur x ou y
}
if (capacity_line[1]) {
abline(v = x$populations[[xpop]]$capacity, lty = capacity_lty[1], col = call_par$col[xpop])
}
if (capacity_line[2]) {
abline(h = x$populations[[ypop]]$capacity, lty = capacity_lty[2], col = call_par$col[ypop])
}
if (text_print[1]) {
text(
x = x$populations[[xpop]]$capacity, y = call_par$ylim[1],
paste("K", x$populations[[xpop]]$label, sep = " "),
pos = 4, srt = 90, col = call_par$col[xpop]
)
}
if (text_print[2]) {
text(
x = call_par$xlim[1], y = x$populations[[ypop]]$capacity,
paste("K", x$populations[[ypop]]$label, sep = " "),
pos = 4, col = call_par$col[ypop]
)
}
}
BEE-Univ-Grenoble/BeePODYNA documentation built on Dec. 25, 2019, 4:49 a.m.
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Defines functions plot.population plot.community com_plot
Documented in com_plot plot.community plot.population
#' @import graphics
#' @import grDevices
NULL
#' plot_population
#'
#' plot one given population and its capacity line.
#'
#' @param x a population object
#' @param ... every argument for the \code{\link[graphics]{plot}} function such as graphical parameters for lines.
#' Classical \code{\link[graphics]{graphical parameter}} applies on the population curve, NOT on the capacity line (custom parameter need to be given, as exemple capacity_lty).
#' \itemize{
#' \item \strong{type} for the size line, set to \code{'b'} by default.
#' \item \strong{xlab} set to \code{'Time'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{ylab} set to \code{'Size'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{main} set to use the pop label by default, see \code{\link[graphics]{title}}.
#' }
#' @param capacity_line set to \code{TRUE} by default, if a dashed line must be drawned to show the capacity.
#' @param capacity_lty set to \code{3} by default.
#' @param text_print set to \code{TRUE} by default, whether there is a text on the capacipty line or not (writting population 'K label' by default).
#' @param add set to \code{FALSE} by default, to add another population plot on a precedent one.
#'
#'
#' @seealso
#' \itemize{
#' \item \code{\link[graphics]{plot}}, \code{\link[graphics]{title}} and \code{\link[graphics]{par}} for plot parameter that were omitted on this documentation
#' \item \code{\link[BeePODYNA]{population}} for every aspect about population and community creations.
#' }
#'
#' @examples
#' data(hudson)
#' hare <- hudson$hare
#' lynx <- hudson$lynx
#'
#' plot(hare,
#' col = "red", pch = 15, type = "b", capacity_lty = 3,
#' lty = 2, main = "Hudson data"
#' )
#'
#' plot(lynx,
#' col = "blue", pch = 15, type = "b", capacity_lty = 3,
#' add = TRUE, lty = 1, capacity_line = TRUE
#' )
#' @author Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>
#'
#' @export
plot.population <- function(x,
...,
capacity_line = TRUE,
capacity_lty = 3,
text_print = TRUE,
add = FALSE) {
delta_x <- (max(x$time) - min(x$time)) * 0.1
delta_y <- (max(x$size) - min(x$size)) * 0.2
default_par <- list(
col = 1,
type = "b",
xlab = "Time",
ylab = "Population size",
main = x$label,
xlim = c(min(x$time) - delta_x, max(x$time) + delta_x),
ylim = c(min(x$size) - delta_y, max(x$size) + delta_y)
)
call_par <- list(...)
names_defaut_par <- names(default_par)
for (i in seq_along(default_par)) {
if (!names_defaut_par[i] %in% names(call_par) | is.null(call_par[[names_defaut_par[i]]])) {
call_par[[names_defaut_par[i]]] <- default_par[[names_defaut_par[i]]]
}
}
if ("log" %in% names(call_par)) {
call_par$log <- sub("x", "", call_par$log)
if (regexec("y", call_par$log)[[1]] > 0) {
if (default_par$ylim[1] < 0) call_par$ylim[1] <- 1
}
}
if (!add) {
empty_par <- c(list(x = 1, y = 1), call_par)
empty_par$type <- "n"
do.call(plot, empty_par)
}
line_par <- c(list(x = x$time, y = x$size), call_par)
line_par$xlim <- NULL
line_par$xlim <- NULL
line_par$ylim <- NULL
line_par$xlab <- NULL
line_par$ylab <- NULL
line_par$main <- NULL
line_par$log <- NULL
do.call(lines, line_par)
if (capacity_line) {
abline(h = x$capacity, lty = capacity_lty, col = call_par$col)
}
if (text_print) {
text(
x = x$time[1], y = x$capacity,
paste("K", x$label, sep = " "),
pos = 3,
col = call_par$col
)
}
}
#' plot.community
#'
#' plot one given community and its capacity line.
#'
#' @param x a community object
#' @param ... every argument for the \code{\link[graphics]{plot}} function such as graphical parameters for lines.
#' Classical \code{\link[graphics]{graphical parameter}} applies on the population curve, NOT on the capacity line (custom parameter need to be given, as exemple capacity_lty).
#' \itemize{
#' \item \strong{type} for the size line, set to \code{'b'} by default.
#' \item \strong{xlab} set to \code{'Time'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{ylab} set to \code{'Size'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{main} set to use the pop label by default, see \code{\link[graphics]{title}}.
#' }
#' @param capacity_line set to \code{TRUE} by default, if a dashed line must be drawned to show the capacity.
#' @param capacity_lty set to \code{3} by default.
#' @param text_print set to \code{TRUE} by default, whether there is a text on the capacipty line or not (writting population 'K label' by default).
#' @param add set to \code{FALSE} by default, to add another population plot on a precedent one.
#'
#' @note For \strong{capacity_line}, \strong{capacity_lty}, \strong{type}, \strong{text_print} and \strong{text_x} parameters, values can be a single value or a vector of value. If the vector length is inferior to the population number in the community, the value or the vector will be copy.
#'
#' @seealso
#' \itemize{
#' \item \code{\link[graphics]{plot}}, \code{\link[graphics]{title}} and \code{\link[graphics]{par}} for plot parameter that were omitted on this documentation
#' \item \code{\link[BeePODYNA]{plot.population}}, \code{\link[BeePODYNA]{population}}, \code{\link[BeePODYNA]{community}} for every aspect about population and community creations.
#' }
#'
#' @import graphics
#'
#' @examples
#' data(hudson)
#' plot(hudson)
#' @author Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>
#'
#' @export
plot.community <- function(x, ...,
capacity_line = TRUE,
capacity_lty = 3,
text_print = TRUE,
add = FALSE) {
n_pop <- length(x)
capacity_line <- rep(capacity_line, n_pop)
capacity_lty <- rep(capacity_lty, n_pop)
text_print <- rep(text_print, n_pop)
com_time <- unlist(sapply(x$populations, "[[", 3))
delta_x <- (max(com_time) - min(com_time))
if(delta_x == 0) delta_x <- 0.1 else delta_x <- delta_x * 0.1
com_size <- unlist(sapply(x$populations, "[[", 2))
delta_y <- (max(com_size) - min(com_size)) * 0.1
if(delta_y == 0) delta_y <- 0.1 else delta_y <- delta_y * 0.1
default_par <- list(
col = rep(1, n_pop),
type = rep("b", n_pop),
xlab = "Time",
ylab = "Population size",
main = x$label,
xlim = c(min(com_time) - delta_x, max(com_time) + delta_x),
ylim = c(min(com_size) - delta_y, max(com_size) + delta_y)
)
call_par <- list(...)
names_defaut_par <- names(default_par)
for (i in seq_along(default_par)) {
if (!names_defaut_par[i] %in% names(call_par) | is.null(call_par[[names_defaut_par[i]]])) {
call_par[[names_defaut_par[i]]] <- default_par[[names_defaut_par[i]]]
}
}
for (i in seq_along(call_par)) {
if(length(call_par[[i]]) < n_pop) call_par[[i]] <- rep(call_par[[i]], n_pop)
}
if ("log" %in% names(call_par)) {
call_par$log <- paste(sub("x", "", call_par$log), collapse = "")
if (regexec("y", call_par$log)[[1]] > 0) {
if (default_par$ylim[1] < 0) call_par$ylim[1] <- 1
}
}
if (!add) {
empty_par <- c(list(x = 1, y = 1), call_par)
tmpx <- empty_par$xlim[1:2]
tmpy <- empty_par$ylim[1:2]
empty_par <- lapply(empty_par, FUN = function(x) x[1])
empty_par$xlim <- tmpx
empty_par$ylim <- tmpy
empty_par$type <- "n"
do.call(plot, empty_par)
}
for (i in 1:n_pop) {
line_par <- call_par
line_par <- lapply(line_par, FUN = function(x) x[i])
line_par <- c(list(x = x$populations[[i]]$time, y = x$populations[[i]]$size), line_par)
line_par$xlim <- NULL
line_par$xlim <- NULL
line_par$ylim <- NULL
line_par$xlab <- NULL
line_par$ylab <- NULL
line_par$main <- NULL
line_par$log <- NULL
do.call(lines, line_par)
if (capacity_line[i]) {
abline(h = x$populations[[i]]$capacity, lty = capacity_lty[i], col = call_par$col[i])
}
if (text_print[i]) {
text(
x = x$populations[[i]]$time[1], y = x$populations[[i]]$capacity,
paste("K", x$populations[[i]]$label, sep = " "),
pos = 3,
col = call_par$col[i]
)
}
}
}
#' com_plot
#'
#' plot a given community of length = 2 with 2 dimmensionnal place.
#'
#' @param x a community object
#' @param ... every argument for the \code{\link[graphics]{plot}} function such as titles, labels and windows limitation.
#' Classical \code{\link[graphics]{graphical parameter}} applies on the population curve, NOT on the capacity line (custom parameter need to be given, as exemple capacity_lty).
#' \itemize{
#' \item \strong{xlab} set to \code{'Time'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{ylab} set to \code{'Size'} by default, see \code{\link[graphics]{title}}.
#' \item \strong{main} set to use the pop label by default, see \code{\link[graphics]{title}}.
#' }
#' @param xpop the population for the x axise
#' @param ypop the population for the y axise
#' @param capacity_line set to \code{TRUE} by default, if a dashed line must be drawned to show the capacity.
#' @param capacity_lty set to \code{3} by default.
#' @param text_print set to \code{TRUE} by default, whether there is a text on the capacipty line or not (writting population 'K label' by default).
#' @param first_p the first point in the time serie to be drawn. All points are drawn by default.
#' @param white the percentage of white for the beginning of the color scale. \code{0.8} by default.
#' @param add set to \code{FALSE} by default, to add another com_plot plot on a precedent one.
#'
#' @note For \strong{capacity_line}, \strong{capacity_lty} and \strong{text_print} parameters, values can be a single value or a vector of value. If the vector length is inferior to the population number in the community, the value or the vector will be copy.
#'
#' @seealso
#' \itemize{
#' \item \code{\link[graphics]{plot}}, \code{\link[graphics]{title}} and \code{\link[graphics]{par}} for plot parameter that were omitted on this documentation
#' \item \code{\link[BeePODYNA]{plot.population}}, \code{\link[BeePODYNA]{population}}, \code{\link[BeePODYNA]{community}} for every aspect about population and community creations.
#' }
#'
#' @import graphics
#'
#' @examples
#' data(hudson)
#' com_plot(hudson)
#' @author Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>
#'
#' @export
com_plot <- function(x, ...,
xpop = 1,
ypop = 2,
capacity_line = c(TRUE, TRUE),
capacity_lty = c(3, 3),
text_print = c(TRUE, TRUE),
first_p = 1,
white = 0.8,
add = FALSE) {
n_pop <- length(x)
capacity_line <- rep(capacity_line, n_pop)
capacity_lty <- rep(capacity_lty, n_pop)
text_print <- rep(text_print, n_pop)
com_x <- x$populations[[xpop]]$size
delta_x <- (max(com_x) - min(com_x))
if (delta_x == 0) delta_x <- 0.1 else delta_x <- delta_x * 0.1
com_y <- x$populations[[ypop]]$size
delta_y <- (max(com_y) - min(com_y)) * 0.1
if (delta_y == 0) delta_y <- 0.1 else delta_y <- delta_y * 0.1
default_par <- list(
col = rep(1, n_pop),
type = rep("b", n_pop),
xlab = x$populations[[xpop]]$label,
ylab = x$populations[[ypop]]$label,
main = x$label,
xlim = c(min(com_x) - delta_x, max(com_x) + delta_x),
ylim = c(min(com_y) - delta_y, max(com_y) + delta_y)
)
call_par <- list(...)
names_defaut_par <- names(default_par)
for (i in seq_along(default_par)) {
if (!names_defaut_par[i] %in% names(call_par) | is.null(call_par[[names_defaut_par[i]]])) {
call_par[[names_defaut_par[i]]] <- default_par[[names_defaut_par[i]]]
}
}
for (i in seq_along(call_par)) {
if (length(call_par[[i]]) < n_pop) call_par[[i]] <- rep(call_par[[i]], n_pop)
}
if ("log" %in% names(call_par)) {
tmp_y <- paste(sub("x","", call_par$log), collapse = "")
if (regexec("y", tmp_y)[[1]] > 0) {
if (default_par$ylim[1] < 0) call_par$ylim[1] <- 1
}
tmp_x <- paste(sub("y","", call_par$log), collapse = "")
if (regexec("x", tmp_x)[[1]] > 0) {
if (default_par$xlim[1] < 0) call_par$xlim[1] <- 1
}
}
if (!add) {
empty_par <- c(list(x = 1, y = 1), call_par)
tmpx <- empty_par$xlim[1:2]
tmpy <- empty_par$ylim[1:2]
empty_par <- lapply(empty_par, FUN = function(x) x[1])
empty_par$xlim <- tmpx
empty_par$ylim <- tmpy
empty_par$type <- "n"
do.call(plot, empty_par)
}
com_time <- 1
x_size <- x$populations[[xpop]]$size
y_size <- x$populations[[ypop]]$size
x_time <- x$populations[[ypop]]$time
# color gradient, only gray for the moment
gray <- gray.colors(length(x_size), start = white, end = 0, gamma = 2.2)
for (i in first_p:length(x_size)) {
segments(
x0 = x_size[i], y0 = y_size[i],
x1 = x_size[i + 1], y1 = y_size[i + 1],
col = gray[i]
)
text(
x = x_size[i], y = y_size[i],
label = x_time[i], col = gray[i], pos = 3
) # modifier pour dire si on prend le time sur x ou y
}
if (capacity_line[1]) {
abline(v = x$populations[[xpop]]$capacity, lty = capacity_lty[1], col = call_par$col[xpop])
}
if (capacity_line[2]) {
abline(h = x$populations[[ypop]]$capacity, lty = capacity_lty[2], col = call_par$col[ypop])
}
if (text_print[1]) {
text(
x = x$populations[[xpop]]$capacity, y = call_par$ylim[1],
paste("K", x$populations[[xpop]]$label, sep = " "),
pos = 4, srt = 90, col = call_par$col[xpop]
)
}
if (text_print[2]) {
text(
x = call_par$xlim[1], y = x$populations[[ypop]]$capacity,
paste("K", x$populations[[ypop]]$label, sep = " "),
pos = 4, col = call_par$col[ypop]
)
}
}
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