441 lines
14 KiB
Plaintext
441 lines
14 KiB
Plaintext
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\documentclass[article,nojss]{jss}
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\DeclareGraphicsExtensions{.pdf,.eps}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Add-on packages and fonts
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\usepackage{amsmath}
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\usepackage{xspace}
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\usepackage{verbatim}
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\usepackage[english]{babel}
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%\usepackage{mathptmx}
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%\usepackage{helvet}
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\usepackage[T1]{fontenc}
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\usepackage[latin1]{inputenc}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
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\newcommand{\di}{\textbf{\textsf{diagram}}\xspace}
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\title{\proglang{R} Package \pkg{shape}: functions for plotting graphical shapes, colors...}
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\Plaintitle{R Package shape: functions for plotting graphical shapes, colors...}
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\Keywords{graphics, shapes, colors, R}
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\Plainkeywords{graphics, shapes, colors, R}
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\author{Karline Soetaert\\
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Royal Netherlands Institute of Sea Research\\
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Yerseke, The Netherlands
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}
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\Plainauthor{Karline Soetaert}
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\Abstract{This document describes how to use the \pkg{shape} package
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for plotting graphical shapes.
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Together with R-package \pkg{diagram} \citep{diagram} this package has
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been written to produce the figures of the book \citep{Soetaertbook}
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}
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%% The address of (at least) one author should be given
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%% in the following format:
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\Address{
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Karline Soetaert\\
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Royal Netherlands Institute of Sea Research (NIOZ)\\
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4401 NT Yerseke, Netherlands
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E-mail: \email{karline.soetaert@nioz.nl}\\
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URL: \url{http://www.nioz.nl}\\
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}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% R/Sweave specific LaTeX commands.
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%% need no \usepackage{Sweave}
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%\VignetteIndexEntry{shape: functions for plotting graphical shapes}
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%\VignetteKeywords{graphics, shapes, colors}
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%\VignettePackage{shape}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Begin of the document
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\begin{document}
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\SweaveOpts{engine=R,eps=FALSE}
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\SweaveOpts{keep.source=TRUE}
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<<preliminaries,echo=FALSE,results=hide>>=
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library("shape")
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options(prompt = "> ")
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options(width=90)
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@
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\maketitle
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\section{Introduction}
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This vignette is the Sweave application of parts of demo
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\code{colorshapes} in package \pkg{shape} \citep{shape}.
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\section{colors}
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Although one can find similar functions in other packages (including the R
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base package \citep{R2008}),
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\pkg{shape} includes ways to generate color schemes;
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\begin{itemize}
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\item \code{intpalette} creates transitions
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between several colors;
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\item \code{shadepalette} creates a gradient between two colors,
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useful for shading (see below).
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\item \code{drapecol} drapes colors over a \code{persp} plot;
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\end{itemize}
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by default the red-blue-yellow (matlab-type) colors are used.
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The code below demonstrates these functions (Figure \ref{fig:s1})
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<<label=s1, include=FALSE>>=
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par(mfrow = c(2, 2))
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image(matrix(nrow = 1, ncol = 50, data = 1:50),
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main = "intpalette",
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col = intpalette(c("red", "blue", "yellow", "green", "black"),
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numcol = 50))
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#
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shadepalette(n = 10, "white", "black")
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#
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image(matrix(nrow = 1, ncol = 50, data = 1:50),
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col = shadepalette(50, "red", "blue"),
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main = "shadepalette")
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#
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par(mar = c(0, 0, 0, 0))
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persp(volcano, theta = 135, phi = 30, col = drapecol(volcano),
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main = "drapecol", border = NA)
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@
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\begin{figure}
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\begin{center}
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<<label=s1, fig=TRUE,echo=FALSE>>=
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<<s1>>
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@
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\end{center}
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\caption{Use of \code{intpalette}, \code{shadepalette} and \code{drapecol}}
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\label{fig:s1}
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\end{figure}
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\section{Rotating}
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Function \code{rotatexy} rotates graphical shapes; it can be used to generate
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strangely-colored shapes (Figure \ref{fig:s2}).
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<<label=s2, include=FALSE>>=
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par(mfrow = c(2, 2), mar = c(3, 3, 3, 3))
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#
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# rotating points on a line
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#
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xy <- matrix(ncol = 2, data = c(1:5, rep(1, 5)))
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plot(xy, xlim = c(-6, 6), ylim = c(-6, 6), type = "b",
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pch = 16, main = "rotatexy", col = 1)
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for (i in 1:5)
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points(rotatexy(xy, mid = c(0, 0), angle = 60*i),
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col = i+1, type = "b", pch = 16)
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points(0, 0, cex = 2, pch = 22, bg = "black")
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legend("topright", legend = 60*(0:5), col = 1:6, pch = 16,
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title = "angle")
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legend("topleft", legend = "midpoint", pt.bg = "black",
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pt.cex = 2, pch = 22, box.lty = 0)
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#
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# rotating lines..
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#
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x <- seq(0, 2*pi, pi/20)
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y <- sin(x)
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cols <- intpalette(c("blue", "green", "yellow", "red"), n = 125)
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cols <- c(cols, rev(cols))
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plot(x, y, type = "l", ylim = c(-3, 3), main = "rotatexy",
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col = cols[1], lwd = 2, xlim = c(-1, 7))
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for (i in 2:250)
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lines(rotatexy(cbind(x, y), angle = 0.72*i), col = cols[i], lwd = 2)
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#
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#
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x <- seq(0, 2*pi, pi/20)
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y <- sin(x*2)
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cols <- intpalette(c("red", "yellow", "black"), n = 125)
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cols <- c(cols, rev(cols))
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plot(x, y, type = "l", ylim = c(-4, 5), main = "rotatexy,
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asp = TRUE", col = cols[1], lwd = 2, xlim = c(-1, 7))
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for (i in 2:250)
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lines(rotatexy(cbind(x, y), angle = 0.72*i, asp = TRUE),
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col = cols[i], lwd = 2)
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#
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# rotating points
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#
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cols <- femmecol(500)
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plot(x, y, xlim = c(-1, 1), ylim = c(-1, 1), main = "rotatexy",
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col = cols[1], type = "n")
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for (i in 2:500) {
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xy <- rotatexy(c(0, 1), angle = 0.72*i, mid = c(0, 0))
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points(xy[1], xy[2], col = cols[i], pch = ".", cex = 2)
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}
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@
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\begin{figure}
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\begin{center}
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<<label=s2,fig=TRUE,echo=FALSE>>=
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<<s2>>
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@
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\end{center}
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\caption{Four examples of \code{rotatexy}}
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\label{fig:s2}
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\end{figure}
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\section{ellipses}
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If a suitable shading color is used, function \code{filledellipse} creates spheres,
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ellipses, donuts with 3-D appearance (Figure \ref{fig:s3}).
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<<label=s3, include=FALSE>>=
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par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
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emptyplot(c(-1, 1))
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col <- c(rev(greycol(n = 30)), greycol(30))
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filledellipse(rx1 = 1, rx2 = 0.5, dr = 0.1, col = col)
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title("filledellipse")
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#
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emptyplot(c(-1, 1), c(-1, 1))
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filledellipse(col = col, dr = 0.1)
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title("filledellipse")
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#
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color <-gray(seq(1, 0.3, length.out = 30))
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emptyplot(xlim = c(-2, 2), ylim = c(-2, 2), col = color[length(color)])
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filledellipse(rx1 = 2, ry1 = 0.4, col = color, angle = 45, dr = 0.1)
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filledellipse(rx1 = 2, ry1 = 0.4, col = color, angle = -45, dr = 0.1)
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filledellipse(rx1 = 2, ry1 = 0.4, col = color, angle = 0, dr = 0.1)
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filledellipse(rx1 = 2, ry1 = 0.4, col = color, angle = 90, dr = 0.1)
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title("filledellipse")
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#
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emptyplot(main = "getellipse")
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col <-femmecol(90)
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for (i in seq(0, 180, by = 2))
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lines(getellipse(0.5, 0.25, mid = c(0.5, 0.5), angle = i, dr = 0.1),
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type = "l", col = col[(i/2)+1], lwd = 2)
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@
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\begin{figure}
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\begin{center}
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<<label=s3, fig=TRUE, echo=FALSE>>=
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<<s3>>
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@
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\end{center}
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\caption{Use of \code{filledellipse}, and \code{getellipse}}
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\label{fig:s3}
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\end{figure}
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\section{Cylinders, rectangles, multigonals}
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The code below draws cylinders, rectangles and multigonals (Figure \ref{fig:s4}).
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<<label=s4, include=FALSE>>=
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par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
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#
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# simple cylinders
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emptyplot(c(-1.2, 1.2), c(-1, 1), main = "filledcylinder")
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col <- c(rev(greycol(n = 20)), greycol(n = 20))
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col2 <- shadepalette("red", "blue", n = 20)
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col3 <- shadepalette("yellow", "black", n = 20)
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filledcylinder(rx = 0., ry = 0.2, len = 0.25, angle = 0,
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col = col, mid = c(-1, 0), dr = 0.1)
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filledcylinder(rx = 0.0, ry = 0.2, angle = 90, col = col,
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mid = c(-0.5, 0), dr = 0.1)
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filledcylinder(rx = 0.1, ry = 0.2, angle = 90, col = c(col2, rev(col2)),
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mid = c(0.45, 0), topcol = col2[10], dr = 0.1)
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filledcylinder(rx = 0.05, ry = 0.2, angle = 90, col = c(col3, rev(col3)),
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mid = c(0.9, 0), topcol = col3[10], dr = 0.1)
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filledcylinder(rx = 0.1, ry = 0.2, angle = 90, col = "white",
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lcol = "black", lcolint = "grey", dr = 0.1)
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#
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# more complex cylinders
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emptyplot(c(-1, 1), c(-1, 1), main = "filledcylinder")
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col <- shadepalette("blue", "black", n = 20)
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col2 <- shadepalette("red", "black", n = 20)
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col3 <- shadepalette("yellow", "black", n = 20)
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filledcylinder(rx = 0.025, ry = 0.2, angle = 90,
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col = c(col2, rev(col2)), dr = 0.1, mid = c(-0.8, 0),
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topcol = col2[10], delt = -1., lcol = "black")
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filledcylinder(rx = 0.1, ry = 0.2, angle = 00,
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col = c(col, rev(col)), dr = 0.1, mid = c(0.0, 0.0),
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topcol = col, delt = -1.2, lcol = "black")
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filledcylinder(rx = 0.075, ry = 0.2, angle = 90,
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col = c(col3, rev(col3)), dr = 0.1, mid = c(0.8, 0),
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topcol = col3[10], delt = 0.0, lcol = "black")
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#
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# rectangles
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color <- shadepalette(grey(0.3), "blue", n = 20)
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emptyplot(c(-1, 1), main = "filledrectangle")
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filledrectangle(wx = 0.5, wy = 0.5, col = color,
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mid = c(0, 0), angle = 0)
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filledrectangle(wx = 0.5, wy = 0.5, col = color,
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mid = c(0.5, 0.5), angle = 90)
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filledrectangle(wx = 0.5, wy = 0.5, col = color,
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mid = c(-0.5, -0.5), angle = -90)
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filledrectangle(wx = 0.5, wy = 0.5, col = color,
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mid = c(0.5, -0.5), angle = 180)
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filledrectangle(wx = 0.5, wy = 0.5, col = color,
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mid = c(-0.5, 0.5), angle = 270)
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#
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# multigonal
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color <- shadepalette(grey(0.3), "blue", n = 20)
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emptyplot(c(-1, 1))
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filledmultigonal(rx = 0.25, ry = 0.25,
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col = shadepalette(grey(0.3), "blue", n = 20),
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nr = 3, mid = c(0, 0), angle = 0)
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filledmultigonal(rx = 0.25, ry = 0.25,
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col = shadepalette(grey(0.3), "darkgreen", n = 20),
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nr = 4, mid = c(0.5, 0.5), angle = 90)
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filledmultigonal(rx = 0.25, ry = 0.25,
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col = shadepalette(grey(0.3), "orange", n = 20),
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nr = 5, mid = c(-0.5, -0.5), angle = -90)
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filledmultigonal(rx = 0.25, ry = 0.25, col = "black",
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nr = 6, mid = c(0.5, -0.5), angle = 180)
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filledmultigonal(rx = 0.25, ry = 0.25, col = "white", lcol = "black",
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nr = 7, mid = c(-0.5, 0.5), angle = 270)
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title("filledmultigonal")
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@
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\begin{figure}
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\begin{center}
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<<label = s4, fig = TRUE,echo = FALSE>>=
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<<s4>>
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@
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\end{center}
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\caption{Use of \code{filledcylinder}, \code{filledrectangle} and
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\code{filledmultigonal}}
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\label{fig:s4}
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\end{figure}
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\section{Other shapes}
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Function \code{filledshape} is the most flexible drawing function from
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\pkg{shape}: just specify an inner and outer shape and
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fill with a color scheme (Figure \ref{fig:s5}).
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<<label = s5, include = FALSE>>=
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par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
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#an egg
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color <- greycol(30)
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emptyplot(c(-3.2, 3.2), col = color[length(color)],
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main = "filledshape")
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b <- 4
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a <- 9
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x <- seq(-sqrt(a), sqrt(a), by = 0.1)
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g <- b-b/a*x^2-0.2*b*x+0.2*b/a*x^3
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g[g<0] <- 0
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x1 <- c(x, rev(x))
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g1 <- c(sqrt(g), rev(-sqrt(g)))
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xouter <- cbind(x1, g1)
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xouter <- rbind(xouter, xouter[1, ])
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filledshape(xouter, xyinner = c(-1, 0), col = color)
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#
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|
|
# a mill
|
||
|
|
color <- shadepalette(grey(0.3), "yellow", n = 20)
|
||
|
|
emptyplot(c(-3.3, 3.3), col = color[length(color)],
|
||
|
|
main = "filledshape")
|
||
|
|
x <- seq(0, 0.8*pi, pi/20)
|
||
|
|
y <- sin(x)
|
||
|
|
xouter <- cbind(x, y)
|
||
|
|
for (i in seq(0, 360, 60))
|
||
|
|
xouter <- rbind(xouter,
|
||
|
|
rotatexy(cbind(x, y), mid = c(0, 0), angle = i))
|
||
|
|
filledshape(xouter, c(0, 0), col = color)
|
||
|
|
#
|
||
|
|
# abstract art
|
||
|
|
emptyplot(col = "darkgrey", main = "filledshape")
|
||
|
|
filledshape(matrix(nc = 2, runif(80)), col = "darkblue")
|
||
|
|
#
|
||
|
|
emptyplot(col = "darkgrey", main = "filledshape")
|
||
|
|
filledshape(matrix(nc = 2, runif(80)),
|
||
|
|
col = shadepalette(20, "darkred", "darkblue"))
|
||
|
|
@
|
||
|
|
\begin{figure}
|
||
|
|
\begin{center}
|
||
|
|
<<label = s5, fig=TRUE, echo=FALSE>>=
|
||
|
|
<<s5>>
|
||
|
|
@
|
||
|
|
\end{center}
|
||
|
|
\caption{Use of \code{filledshape}}
|
||
|
|
\label{fig:s5}
|
||
|
|
\end{figure}
|
||
|
|
|
||
|
|
\section{arrows, arrowheads}
|
||
|
|
As the arrow heads in the R base package are too simple for some applications,
|
||
|
|
there are some improved arrow heads in \pkg{shape} (Figure \ref{fig:s6}).
|
||
|
|
<<label = s6, include=FALSE>>=
|
||
|
|
par(mfrow = c(2, 2), mar = c(2, 2, 2, 2))
|
||
|
|
xlim <- c(-5 , 5)
|
||
|
|
ylim <- c(-10, 10)
|
||
|
|
x0<-runif(100, xlim[1], xlim[2])
|
||
|
|
y0<-runif(100, ylim[1], ylim[2])
|
||
|
|
x1<-x0+runif(100, -2, 2)
|
||
|
|
y1<-y0+runif(100, -2, 2)
|
||
|
|
size <- 0.4
|
||
|
|
plot(0, type = "n", xlim = xlim, ylim = ylim)
|
||
|
|
Arrows(x0, y0, x1, y1, arr.length = size, arr.type = "triangle",
|
||
|
|
arr.col = rainbow(runif(100, 1, 20)))
|
||
|
|
title("Arrows")
|
||
|
|
#
|
||
|
|
# arrow heads
|
||
|
|
#
|
||
|
|
ang <- runif(100, -360, 360)
|
||
|
|
plot(0, type = "n", xlim = xlim, ylim = ylim)
|
||
|
|
Arrowhead(x0, y0, ang, arr.length = size, arr.type = "curved",
|
||
|
|
arr.col = rainbow(runif(100, 1, 20)))
|
||
|
|
title("Arrowhead")
|
||
|
|
#
|
||
|
|
# Lotka-Volterra competition model
|
||
|
|
#
|
||
|
|
r1 <- 3 # parameters
|
||
|
|
r2 <- 2
|
||
|
|
K1 <- 1.5
|
||
|
|
K2 <- 2
|
||
|
|
alf12 <- 1
|
||
|
|
alf21 <- 2
|
||
|
|
|
||
|
|
xlim <- c(0, 1.5)
|
||
|
|
ylim <- c(0, 2 )
|
||
|
|
par(mar = c(5, 4, 4, 2))
|
||
|
|
plot (0, type = "l", lwd = 3, # 1st isocline
|
||
|
|
main = "Lotka-Volterra competition",
|
||
|
|
xlab = "N1", ylab = "N2", xlim = xlim, ylim = ylim)
|
||
|
|
|
||
|
|
gx <- seq(0, 1.5, len = 30)
|
||
|
|
gy <- seq(0, 2, len = 30)
|
||
|
|
N <- as.matrix(expand.grid(x = gx, y = gy))
|
||
|
|
|
||
|
|
dN1 <- r1*N[, 1]*(1-(N[, 1]+alf12* N[, 2])/K1)
|
||
|
|
dN2 <- r2*N[, 2]*(1-(N[, 2]+alf21* N[, 1])/K2)
|
||
|
|
dt <- 0.01
|
||
|
|
Arrows(N[, 1], N[, 2], N[, 1]+dt*dN1, N[, 2]+dt*dN2, arr.len = 0.08,
|
||
|
|
lcol = "darkblue", arr.type = "triangle")
|
||
|
|
points(x = c(0, 0, 1.5, 0.5), y = c(0, 2, 0, 1), pch = 22, cex = 2,
|
||
|
|
bg = c("white", "black", "black", "grey"))
|
||
|
|
|
||
|
|
@
|
||
|
|
\begin{figure}
|
||
|
|
\begin{center}
|
||
|
|
<<label = s6, fig=TRUE,echo=FALSE>>=
|
||
|
|
<<s6>>
|
||
|
|
@
|
||
|
|
\end{center}
|
||
|
|
\caption{Use of \code{Arrows} and \code{Arrowhead} }
|
||
|
|
\label{fig:s6}
|
||
|
|
\end{figure}
|
||
|
|
|
||
|
|
\section{Miscellaneous}
|
||
|
|
Since version 1.3.4, function \code{textflag} has been added.
|
||
|
|
<<label = textflag, include=FALSE>>=
|
||
|
|
emptyplot()
|
||
|
|
textflag(mid = c(0.5, 0.5), radx = 0.5, rady = 0.2,
|
||
|
|
lcol = "white", lab = "hello", cex = 5, font = 2:3)
|
||
|
|
@
|
||
|
|
\setkeys{Gin}{width=0.8\textwidth}
|
||
|
|
\begin{figure}[ht]
|
||
|
|
\begin{center}
|
||
|
|
<<label = textflag, fig=TRUE,echo=FALSE, width = 12, height = 6>>=
|
||
|
|
<<textflag>>
|
||
|
|
@
|
||
|
|
\end{center}
|
||
|
|
\caption{Use of function \code{textflag} }
|
||
|
|
\label{fig:textflag}
|
||
|
|
\end{figure}
|
||
|
|
\section{And finally}
|
||
|
|
|
||
|
|
This vignette was created using Sweave \citep{Leisch02}.
|
||
|
|
|
||
|
|
The package is on CRAN, the R-archive website (\citep{R2008})
|
||
|
|
|
||
|
|
More examples can be found in the demo's of package \pkg{ecolMod} \citep{ecolMod}
|
||
|
|
|
||
|
|
\bibliography{vignettes}
|
||
|
|
|
||
|
|
\end{document}
|
||
|
|
|