From 4bb9bab871ad4e7e1770f6eda4626121e7c32589 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <hugo.gruson@protonmail.com>
Date: Mon, 3 Feb 2020 18:52:01 +0100
Subject: [PATCH] Add plot.vismodel()

---
 NAMESPACE            |  1 +
 R/plot.vismodel.R    | 81 ++++++++++++++++++++++++++++++++++++++++++++
 man/plot.vismodel.Rd | 39 +++++++++++++++++++++
 3 files changed, 121 insertions(+)
 create mode 100644 R/plot.vismodel.R
 create mode 100644 man/plot.vismodel.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 943d36d26..3e02f181b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ S3method(merge,rspec)
 S3method(plot,colspace)
 S3method(plot,rimg)
 S3method(plot,rspec)
+S3method(plot,vismodel)
 S3method(points,colspace)
 S3method(subset,colspace)
 S3method(subset,rspec)
diff --git a/R/plot.vismodel.R b/R/plot.vismodel.R
new file mode 100644
index 000000000..d1dc27ac4
--- /dev/null
+++ b/R/plot.vismodel.R
@@ -0,0 +1,81 @@
+#' Title
+#'
+#' @param vismodeldata the result from [vismodel()]. Quantum catches computed
+#'   with another tool are not yet supported.
+#' @param colour.solid logical (defaults to `TRUE`). Should the colour solid for
+#'   the relevant illuminant and visual system be plotted.
+#' @param ... additional arguments passed to [plot()].
+#'
+#' @return
+#'
+#' @export
+#'
+#' @details
+#' This function only works with non-relative quantum catches
+#' (`relative = FALSE` in [vismodel()]) as it would always be the line y = 1 -x
+#' otherwise.
+#'
+#' @examples
+#' data(sicalis)
+#' vis_sicalis <- vismodel(sicalis, "canis", relative = FALSE)
+#' plot(vis_sicalis)
+#'
+#' @references Wilkins, L., & Osorio D. C. (2019). Object colours, material
+#'   properties and animal signals. Journal of Experimental Biologyn 222(21),
+#'   \doi{10.1242/jeb.204487}.
+#'
+plot.vismodel <- function(vismodeldata, colour.solid = TRUE, ...) {
+
+  if (!inherits(vismodeldata, "vismodel")) {
+    stop("'vismodeldata' must be the output from the vismodel() function.")
+  }
+  if (attr(vismodeldata, "conenumb") != 2) {
+    stop("Currently not implemented for anything else than dichromats.")
+  }
+  if (attr(vismodeldata, "relative")) {
+    stop("plot.vismodel() only works with non-relative quantum catches")
+  }
+
+  maxqcatches <- as.data.frame(attr(vismodeldata, "data.maxqcatches"))
+  solid1 <- cumsum(maxqcatches[order(maxqcatches$s / maxqcatches$l), ])
+  solid2 <- cumsum(maxqcatches[order(maxqcatches$l / maxqcatches$s), ])
+  solid <- rbind(solid1, solid2[rev(seq_len(nrow(solid2))), ], c(0, 0))
+
+  arg <- list(...)
+
+  if (is.null(arg$xlab)) {
+    arg$xlab <- "s"
+  }
+  if (is.null(arg$ylab)) {
+    arg$ylab <- "l"
+  }
+  if (is.null(arg$pch)) {
+    arg$pch <- 19
+  }
+  if (is.null(arg$xlim)) {
+    if(colour.solid) {
+      arg$xlim <- c(0, 1)
+    } else {
+      arg$xlim <- c(0, 1.1 * max(vismodeldata$s))
+    }
+  }
+  if (is.null(arg$ylim)) {
+    if(colour.solid) {
+      arg$ylim <- c(0, 1)
+    } else {
+      arg$ylim <- c(0, 1.1 * max(vismodeldata$l))
+    }
+  }
+
+  do.call(plot, c(list(x = NULL), arg))
+
+  if (colour.solid) {
+    polygon(solid, col = "grey", border = NA)
+  }
+
+  arg$x <- vismodeldata$s
+  arg$y <- vismodeldata$l
+
+  do.call(points, arg)
+
+}
diff --git a/man/plot.vismodel.Rd b/man/plot.vismodel.Rd
new file mode 100644
index 000000000..9677d8030
--- /dev/null
+++ b/man/plot.vismodel.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot.vismodel.R
+\name{plot.vismodel}
+\alias{plot.vismodel}
+\title{Title}
+\usage{
+\method{plot}{vismodel}(vismodeldata, colour.solid = TRUE, ...)
+}
+\arguments{
+\item{vismodeldata}{the result from \code{\link[=vismodel]{vismodel()}}. Quantum catches computed
+with another tool are not yet supported.}
+
+\item{colour.solid}{logical (defaults to \code{TRUE}). Should the colour solid for
+the relevant illuminant and visual system be plotted.}
+
+\item{...}{additional arguments passed to \code{\link[=plot]{plot()}}}
+}
+\value{
+
+}
+\description{
+Title
+}
+\details{
+This function only works with non-relative quantum catches
+(\code{relative = FALSE} in \code{\link[=vismodel]{vismodel()}}) as it would always be the line y = 1 -x
+otherwise.
+}
+\examples{
+data(sicalis)
+vis_sicalis <- vismodel(sicalis, "canis", relative = FALSE)
+plot(vis_sicalis)
+
+}
+\references{
+Wilkins, L., & Osorio D. C. (2019). Object colours, material
+properties and animal signals. Journal of Experimental Biologyn 222(21),
+\doi{10.1242/jeb.204487}.
+}