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examples.R
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examples.R
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## fancyaxis: Draw axis which shows minimum, maximum, quartiles
## and mean
##
## 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
## 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
##
## $Id$
source("fancyaxis.R")
opendevice <- function() {
# Background colour
par("bg"="#fffff0")
#par("bg"="transparent")
# Output device. If outputing to a file, remember to use dev.off() at
# the end
#png(file="/tmp/faithful.png",width=480,height=380,bg=par("bg"))
#png(file="/tmp/faithful.png",width=380,height=380,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"))
# 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"))
#X11(bg=par("bg"))
# Make axis labels horizontal
par(las=1)
}
closedevice <- function() {
# Use this if outputing to a file
dev.off()
}
stripchartexample <- function() {
opendevice()
#xdata=iris$Petal.Width
#ydata=iris$Petal.Length
#xdata=cars$speed
#ydata=cars$dist
# Sample dataset from R
xdata <- faithful$waiting
ydata <- faithful$eruptions*60
len=length(xdata)
# Label event with its previous duration
split=180
lag=ydata[1:len-1]
colours <- lag
colours[lag>=split] <- "red"
colours[!(lag>=split)] <- "blue"
xdata=xdata[2:len]
ydata=ydata[2:len]
len=length(xdata)
# Label event age by a colour in the range (0,0.75)
#colours <- gray((1:length(xdata))/length(xdata)*0.75)
# Plot the data
plot(xdata,ydata,
# Omit axes
axes=FALSE,
pch=20,
main=sprintf("Old Faithful Eruptions (%d samples)", len),
xlab="Time till next eruption (min)",
ylab="Duration (sec)",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(70,max(ydata)),
cex=0.5,
col=colours)
axp=par("xaxp")
axp[3] <- axp[3]*2
par("xaxp"=axp)
# Add the axes, passing in the summary to provide quartile and mean
fancyaxis(1,summary(xdata), digits=0)
fancyaxis(2,summary(ydata), digits=0)
# Add the stripcharts
axisstripchart(xdata, 1)
axisstripchart(ydata, 2)
lines(c(min(xdata),max(xdata)),c(split,split),lty=2, col="gray50", xpd=FALSE)
h=par("cxy")[2]/2
points(rep(max(xdata),2),c(split+h,split-h),col=c("red","blue"), pch=20)
text(95,split+h, "Previous duration", adj=c(1,0.5))
closedevice()
}
rugexample <- function() {
opendevice()
#xdata=iris$Petal.Width
#ydata=iris$Petal.Length
#xdata=cars$speed
#ydata=cars$dist
# Sample dataset from R
xdata <- faithful$waiting
ydata <- faithful$eruptions*60
len=length(xdata)
# Label event age by a colour in the range (0,0.75)
#colours <- gray((1:length(xdata))/length(xdata)*0.75)
# Label event with its previous duration
#lag=ydata[1:len-1]
#lma=max(lag)
#lmi=min(lag)
#lag=lag-lmi
#lag=lag/(lma-lmi)
#colours <- gray(c(0,lag))
#colours <- lag
#colours[lag>=180] <- "red"
#colours[!(lag>=180)] <- "blue"
#xdata=xdata[2:len]
#ydata=ydata[2:len]
# Plot the data
plot(xdata,ydata,
# Omit axes
axes=FALSE,
pch=20,
main=sprintf("Old Faithful Eruptions (%d samples)", len),
xlab="Time till next eruption (min)",
ylab="Duration (sec)",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(70,max(ydata)),
cex=0.5)
# Add the axes, passing in the summary to provide quartile and mean
fancyaxis(1,summary(xdata))
fancyaxis(2,summary(ydata))
# This data is heavily rounded and there are lots of ties, so use
# jitter to show distribution. It is not ideal but will do for
# and example
jx <- clippedjitter(xdata, amount=0.4)
jy <- clippedjitter(ydata, amount=0.1)
# Draw the rug for X
minimalrug(jx, side=1, line=-0.8)
# Draw the rug for Y
minimalrug(jy, side=2, line=-0.8)
closedevice()
}
pairexample <- function(){
#opendevice()
# Split the screen in two columns
split.screen(c(1,2))
# Left graph
screen(1)
stripchartexample()
# Right graph
screen(2)
rugexample()
# Tidy up
close.screen(all = TRUE)
#closedevice()
}
multipleexample <- function() {
opendevice()
xdata <- faithful$waiting
ydata <- faithful$eruptions*60
# Split the data in 5 sections
len=length(xdata)
s=floor(len/5)
# Split the screen in 5 columns
par(las=1)
split.screen(c(1,5))
# Image 1
screen(1)
x=xdata[1:s]
y=ydata[1:s]
par(mar=c(5.1, 4.1, 4.1, 2.1))
print(length(x))
plot(x,y,
# Omit axes
axes=FALSE,
pch=20,
xlab="Time till next eruption (min)",
# Normal Y label
ylab="Duration (sec)",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(90,max(ydata)),
cex=0.5,
col="black")
fancyaxis(1,summary(x),digits=0,shiftfac=0.01, gapfac=0.01)
fancyaxis(2,summary(y),digits=0,shiftfac=0.01, gapfac=0.01)
#axisstripchart(x, 1, sshift=0.4)
#axisstripchart(y, 2, sshift=0.4)
# Image 2
screen(2)
x=xdata[(s+1):(2*s)]
y=ydata[(s+1):(2*s)]
par(mar=c(5.1, 4.1, 4.1, 2.1))
print(length(x))
plot(x,y,
# Omit axes
axes=FALSE,
pch=20,
xlab="Time till next eruption (min)",
# Ommit Y label
ylab="",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(90,max(ydata)),
cex=0.5,
col="black")
fancyaxis(1,summary(x),digits=0,shiftfac=0.01, gapfac=0.01)
fancyaxis(2,summary(y),digits=0,shiftfac=0.01, gapfac=0.01)
#axisstripchart(x, 1, sshift=0.4)
#axisstripchart(y, 2, sshift=0.4)
# Image 3
screen(3)
x=xdata[(2*s+1):(3*s)]
y=ydata[(2*s+1):(3*s)]
par(mar=c(5.1, 4.1, 4.1, 2.1))
print(length(x))
plot(x,y,
# Omit axes
axes=FALSE,
pch=20,
# Middle plot, so show title
main="",
xlab="Time till next eruption (min)",
# Ommit Y label
ylab="",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(90,max(ydata)),
cex=0.5,
col="black")
title("Old Faithful Eruptions", xpd=NA)
fancyaxis(1,summary(x),digits=0,shiftfac=0.01, gapfac=0.01)
fancyaxis(2,summary(y),digits=0,shiftfac=0.01, gapfac=0.01)
#axisstripchart(x, 1, sshift=0.4)
#axisstripchart(y, 2, sshift=0.4)
# Image 4
screen(4)
x=xdata[(3*s+1):(4*s)]
y=ydata[(3*s+1):(4*s)]
par(mar=c(5.1, 4.1, 4.1, 2.1))
print(length(x))
plot(x,y,
# Omit axes
axes=FALSE,
pch=20,
xlab="Time till next eruption (min)",
# Ommit Y label
ylab="",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(90,max(ydata)),
cex=0.5,
col="black")
fancyaxis(1,summary(x),digits=0,shiftfac=0.01, gapfac=0.01)
fancyaxis(2,summary(y),digits=0,shiftfac=0.01, gapfac=0.01)
#axisstripchart(x, 1, sshift=0.4)
#axisstripchart(y, 2, sshift=0.4)
# Image 5
screen(5)
x=xdata[(4*s+1):(len)]
y=ydata[(4*s+1):(len)]
par(mar=c(5.1, 4.1, 4.1, 2.1))
print(length(x))
plot(x,y,
# Omit axes
axes=FALSE,
pch=20,
xlab="Time till next eruption (min)",
# Ommit Y label
ylab="",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(90,max(ydata)),
cex=0.5,
col="black")
fancyaxis(1,summary(x),digits=0,shiftfac=0.01, gapfac=0.01)
fancyaxis(2,summary(y),digits=0,shiftfac=0.01, gapfac=0.01)
#axisstripchart(x, 1, sshift=0.4)
#axisstripchart(y, 2, sshift=0.4)
# Cleanup
close.screen(all = TRUE)
closedevice()
}
lagexample <- function() {
opendevice()
#xdata=iris$Petal.Width
#ydata=iris$Petal.Length
#xdata=cars$speed
#ydata=cars$dist
# Sample dataset from R
xdata <- faithful$waiting
ydata <- faithful$eruptions*60
len=length(xdata)
# Label event age by a colour in the range (0,0.75)
#colours <- gray((1:length(xdata))/length(xdata)*0.75)
# Label event with its previous duration
lag=ydata[1:len-1]
lma=max(lag)
lmi=min(lag)
lag=lag-lmi
lag=lag/(lma-lmi)
colours <- gray(lag)
#colours <- lag
#colours[lag>=180] <- "red"
#colours[!(lag>=180)] <- "blue"
xdata=xdata[2:len]
ydata=ydata[2:len]
len=length(xdata)
# Plot the data
plot(xdata,ydata,
# Omit axes
axes=FALSE,
pch=20,
main=sprintf("Old Faithful Eruptions (%d samples)", len),
xlab="Time till next eruption (min)",
ylab="Duration (sec)",
# Leave some space for the rug plot
xlim=c(41,max(xdata)),
ylim=c(90,max(ydata)),
cex=0.5,
col=colours)
# Add the axes, passing in the summary to provide quartile and mean
fancyaxis(1,summary(xdata))
fancyaxis(2,summary(ydata))
closedevice()
}
lagplot <- function() {
opendevice()
ydata <- faithful$eruptions*60
lag.plot(ydata, ann=FALSE, pch=20, cex=0.5, oma=c(1.2,3,2,1))
title(xlab="Lagged duration (sec)")
title(ylab="Duration (sec)")
closedevice()
}