R packaging plus rangeaxis function.

.gitignore

@@ -0,0 +1 @@
+man/.Rhistory

DESCRIPTION

@@ -0,0 +1,10 @@
+Package: fancyaxis
+Version: 0.5
+Date: 2012-06-10
+Title: Functions for drawing scatter-plots and axes inspired by E. Tufte's redesigns.
+Author: Steven J. Murdoch \url{http://www.cl.cam.ac.uk/users/sjm217/}
+Maintainer: Peter N. Steinmetz <[email protected]>
+Description: A set of functions for plotting scatterplots and creating 
+  axes which are inspired by E. Tufte's ""The Visual Display of 
+  Quantitative Information"
+License: GPL version 3 or newer

NAMESPACE

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+export(fancyaxis,axisstripchart,rangeaxis,minimalrug,clippedjitter)

R/axisstripchart.R

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+## Draw a stripchart on an axis, showing marginal frequency
+
+##     Copyright (C) 2005 Steven J. Murdoch <http://www.cl.cam.ac.uk/users/sjm217/>
+##     Permissions at bottom.
+
+##     This is very much a work in progress and still of alpha
+##     quality. See the example file for usage. It currently does not
+##     deal with logarithmic scales properly and needs manual tweaking
+##     of several values to suit different data and output device
+##     resolution. Comments and suggestions are appreciated. My
+##     contact details can be found here:
+##       http://www.cl.cam.ac.uk/users/sjm217/#contact
+##
+##     The design of the graph is based on a scatterplot presented in
+##     "The Visual Display of Quantitative Information", Edward Tufte.
+##     Thanks to Paul Murrell for assistance with handling the log axes
+##
+##     From $Id: fancyaxis.R 6927 2009-03-08 12:49:17Z sjm217 $
+
+axisstripchart <- function(x, side, sshift=0.3) {
+  # x:    the data from which the plots are to be produced.
+  # side: as in axis()
+
+  # Find out the properties of the side we are doing
+  parside <-
+    if (side==1){
+      # Does the outside of the plot have larger or smaller vales
+      flip <- 1
+      # Are we on the yaxis
+      yaxis <- FALSE
+      # Relevant index of par("usr")
+      3
+    }
+    else if (side==2) {
+      flip <- 1
+      yaxis <- TRUE
+      1
+    }
+    else if (side==3) {
+      flip <- -1
+      yaxis <- FALSE
+      4
+    }
+    else if (side==4) {
+      flip <- -1
+      yaxis <- TRUE
+      2
+    }
+
+  # Axis position
+  base<-par("usr")[parside]
+
+  # Width and height in user units
+  plotwidth <- diff(par("usr")[1:2])
+  plotheight <- diff(par("usr")[3:4])
+
+  # Shift for the q2 and q3 axis from the base (in inches)
+  shift <- par("pin")[1]*0.003*flip
+  # Gap for the median
+  gap <- par("pin")[1]*0.003
+  # Shift for the mean pointer away from the axis
+  meanshift <- par("cin")[1]*0.5*flip
+  # Shift away from the q2 and q3 axis for the stripchart
+  stripshift <- par("cin")[1]*sshift*flip
+
+  # Scale lengths so both axes are equal on output device
+  if (yaxis) {
+    shift <- shift/par("pin")[1]*plotwidth
+    meanshift <- meanshift/par("pin")[1]*plotwidth
+    stripshift <- stripshift/par("pin")[1]*plotwidth
+    gap <- gap/par("pin")[2]*plotheight
+  } else {
+    shift <- shift/par("pin")[2]*plotheight
+    meanshift <- meanshift/par("pin")[2]*plotheight
+    stripshift <- stripshift/par("pin")[2]*plotheight
+    gap <- gap/par("pin")[1]*plotwidth
+  }
+
+  # If vertical, stripchart assumes offset is a factor of character
+  # width, if horizontal, character height (bug?). So correct for this
+  if (yaxis)
+    offset=flip*par("cin")[2]/par("cin")[1]
+  else
+    offset=flip
+
+  # Don't clip the chart
+  oldxpd <- par(xpd = TRUE)
+  on.exit(par(oldxpd))
+
+  stripchart(x, method="stack", vertical=yaxis, offset=offset, pch=15,
+             cex=0.2, add=TRUE, at=base+shift+stripshift, col="red")
+}
+
+##     This program is free software; you can redistribute it and/or modify
+##     it under the terms of the GNU General Public License as published by
+##     the Free Software Foundation; either version 2 of the License, or
+##     (at your option) any later version.
+##
+##     This program is distributed in the hope that it will be useful,
+##     but WITHOUT ANY WARRANTY; without even the implied warranty of
+##     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##     GNU General Public License for more details.
+##
+##     You should have received a copy of the GNU General Public License
+##     along with this program; if not, write to the Free Software
+##     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

R/clippedjitter.R

@@ -0,0 +1,72 @@
+##     Copyright (C) 2005 Steven J. Murdoch <http://www.cl.cam.ac.uk/users/sjm217/>
+##     Permissions at bottom.
+##
+##     This is very much a work in progress and still of alpha
+##     quality. See the example file for usage. It currently does not
+##     deal with logarithmic scales properly and needs manual tweaking
+##     of several values to suit different data and output device
+##     resolution. Comments and suggestions are appreciated. My
+##     contact details can be found here:
+##       http://www.cl.cam.ac.uk/users/sjm217/#contact
+##
+##     The design of the graph is based on a scatterplot presented in
+##     "The Visual Display of Quantitative Information", Edward Tufte.
+##     Thanks to Paul Murrell for assistance with handling the log axes
+##
+##     From $Id: fancyaxis.R 6927 2009-03-08 12:49:17Z sjm217 $
+
+# Add a small amount of noise to a numeric vector, preserving minimum
+# and minimum
+clippedjitter <- function(x, ...) {
+  # x:   numeric to which jitter should be added.
+  # ...: parameters passed to jitter()
+
+  mi <- min(x)
+  ma <- max(x)
+
+  len=length(x)
+
+  # Find a position for the min and max
+  mipos <- ((1:len)[x==mi])[1]
+  mapos <- ((1:len)[x==ma])[1]
+
+  # The standard jittered data
+  xj <- jitter(x, ...)
+
+  # Find the elements which are outside the limits
+  under <- xj<mi
+  over <- xj>ma
+
+  # Find the distance away from the limit
+  dunder <- mi-xj[under]
+  dover <- xj[over]-ma
+
+  # Reflect over the limit
+  repunder <- dunder+mi
+  repover <- ma-dover
+
+  # Replace out of limit values with the reflected ones
+  xj[under] <- repunder
+  xj[over] <- repover
+
+  # Replace a jittered min/max with the original min/max
+  xj[mipos] <- mi
+  xj[mapos] <- ma
+
+  # Return updated array
+  xj
+}
+
+##     This program is free software; you can redistribute it and/or modify
+##     it under the terms of the GNU General Public License as published by
+##     the Free Software Foundation; either version 2 of the License, or
+##     (at your option) any later version.
+##
+##     This program is distributed in the hope that it will be useful,
+##     but WITHOUT ANY WARRANTY; without even the implied warranty of
+##     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##     GNU General Public License for more details.
+##
+##     You should have received a copy of the GNU General Public License
+##     along with this program; if not, write to the Free Software
+##     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

examples.R → R/examples.R

@@ -1,21 +1,7 @@
-##     fancyaxis: Draw axis which shows minimum, maximum, quartiles
-##                 and mean
+##     Examples for fancyaxis package.
 ##
 ##     Copyright (C) 2005 Steven J. Murdoch <http://www.cl.cam.ac.uk/users/sjm217/>
-##
-##     This program is free software; you can redistribute it and/or modify
-##     it under the terms of the GNU General Public License as published by
-##     the Free Software Foundation; either version 2 of the License, or
-##     (at your option) any later version.
-##
-##     This program is distributed in the hope that it will be useful,
-##     but WITHOUT ANY WARRANTY; without even the implied warranty of
-##     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-##     GNU General Public License for more details.
-##
-##     You should have received a copy of the GNU General Public License
-##     along with this program; if not, write to the Free Software
-##     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+##     Permissions at bottom.
 
 ##     This is very much a work in progress and still of alpha
 ##     quality. See the example file for usage. It currently does not
@@ -29,9 +15,7 @@
 ##     "The Visual Display of Quantitative Information", Edward Tufte.
 ##     Thanks to Paul Murrell for assistance with handling the log axes
 ##
-##     $Id$
-
-source("fancyaxis.R")
+##     $Id: examples.R 1024 2005-06-16 13:36:05Z sjm217 $
 
 opendevice <- function() {
   # Background colour
@@ -44,10 +28,10 @@ opendevice <- function() {
 
   #png(file="/tmp/faithful.png",width=380,height=380,bg=par("bg"))
 
-  postscript(file="/tmp/faithful.ps",paper="A4",bg=par("bg"))
+  #postscript(file="/tmp/faithful.ps",paper="A4",bg=par("bg"))
 
   # A4 paper
-  #pdf(file="/tmp/faithful.pdf", width=297/25.4, height=210/25.4, bg=par("bg"))
+  pdf(file="faithful.pdf", width=297/25.4, height=210/25.4, bg=par("bg"))
 
   # Wider paper, used for the small multiple graph
   #pdf(file="/tmp/faithful.pdf", width=297/25.4*1.5, height=210/25.4/2, bg=par("bg"))
@@ -409,3 +393,17 @@ lagplot <- function() {
 
   closedevice()
 }
+
+##     This program is free software; you can redistribute it and/or modify
+##     it under the terms of the GNU General Public License as published by
+##     the Free Software Foundation; either version 2 of the License, or
+##     (at your option) any later version.
+##
+##     This program is distributed in the hope that it will be useful,
+##     but WITHOUT ANY WARRANTY; without even the implied warranty of
+##     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##     GNU General Public License for more details.
+##
+##     You should have received a copy of the GNU General Public License
+##     along with this program; if not, write to the Free Software
+##     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA