?Sweave
librar()
library()
source("http://bioconductor.org/biocLite.R")
biocLite()
library(ISwR)
data(cystfiber)
data(cystfibr)
ls()
str(cystfibr)
save(cysfibr,"cysfibr.RData")
save(cysfibr,file="cysfibr.RData")
save(cystfibr,file="cystfibr.RData")
dir()
?Renviron
library(gdata)
?read.xls
library(nlme)
library(ElemStatLearn)
data(ElemStatLearn)
help(ElemStatLearn)
plot(rnorm(100),main="été")
library(tkrplot)
?tkrplot
examples(tkrplot)
examples()
setwd("~/www/articles/r-graphics")
setwd("Users/chl/www/articles/r-graphics")
setwd("/Users/chl/www/articles/r-graphics")
load(".RData")
xx
?round
y <- rnorm(100,0,(1+2*rbinom(100,1,0.35)))
length(y)
?dnorm
x <- y
xx <- seq(min(x),max(x),length=length(x))
length(xx)
length(dnorm(xx,mean=mean(x),sd=sd(x)))
?hist
?desnity
?expression
as.numeric(tclvalue(c(.5,3)))
?tkscale
?warning
source("density_tk.R")
rm(list=ls())
PNG <- FALSE
x <- rnorm(20,mean=20,sd=2.5)
y <- rnorm(20,mean=22,sd=2.3)

if (PNG) png("ex1.png")
boxplot(x,y)
points(c(rep(1,20),rep(2,20)),c(x,y),col='gray50')
points(c(1,2),c(mean(x),mean(y)),pch='x',cex=2,col=c('blue','red'))
if (PNG) dev.off()
?collapse
  y <- rnorm(100)
  x <- gl(4,25,100,labels=paste("g",1:4,sep=""))
  stripchart(y~x,method='stack',vertical=T)
  (moy <- as.numeric(tapply(y,x,mean)))
  points(1:4,moy,pch="X",col='blue',cex=2)
  lines(1:4,moy,col='blue',lwd=2)
  y <- rnorm(1000)
  x <- gl(4,25,1000,labels=paste("g",1:4,sep=""))
  stripchart(y~x,method='stack',vertical=T)
  (moy <- as.numeric(tapply(y,x,mean)))
  points(1:4,moy,pch="X",col='blue',cex=2)
  lines(1:4,moy,col='blue',lwd=2)
?stripchart
  y <- rnorm(1000)
  x <- gl(4,25,1000,labels=paste("g",1:4,sep=""))
  stripchart(y~x,method="jitter",vertical=T)
  (moy <- as.numeric(tapply(y,x,mean)))
  points(1:4,moy,pch="X",col='blue',cex=2)
  lines(1:4,moy,col='blue',lwd=2)
png("ex2.png")
  stripchart(y~x,method="jitter",ylab="Y",xlab="X",vertical=T)
  (moy <- as.numeric(tapply(y,x,mean)))
  points(1:4,moy,pch="X",col='blue',cex=2)
  lines(1:4,moy,col='blue',lwd=2)
getwd()
?rpois
y <- rpois(1000,10)
  stripchart(y~x,method="stack",ylab="Y",xlab="X",vertical=T)
x
png("ex3.png")
  y <- rpois(500,10)
  x <- gl(4,25,500,labels=paste("g",1:4,sep=""))
  stripchart(y~x,method="stack",ylab="Y",xlab="X",vertical=T)
png("ex5.png")
old.par <- par(mar=c(5,4,4,5))#
xx <- c(.2, .5, .8)#
yy <- xx*0.8+0.1#
plot(c(0,1), c(0,1), type="n", axes=FALSE, xlab=expression(Theta), ylab="")#
axis(1, at=xx, labels=c(expression(theta[1]),expression(theta[2]),expression(theta[3])))#
axis(2, at=yy, las=1, labels=c(expression(widehat(y)[1]),#
	expression(widehat(y)[2]),expression(widehat(y)[3])))#
axis(4, at=seq(0,1,by=0.5), las=1)#
box()#
#
abline(0.1,0.8)#
#
#
x <- seq(-3,3,length=100)#
y <- dnorm(x)/2#
threshold <- 0.35#
for (i in 1:3) {#
  y1 <- x/12 + yy[i]#
  x1 <- y + xx[i]#
  lines(x1, y1)#
  whichy <- y1>=threshold#
  new.x1 <- c(xx[i],x1[whichy])#
  new.y1 <- c(y1[whichy][1],y1[whichy])#
  polygon(new.x1, new.y1, col="light blue", border=NA)#
}#
abline(h=yy, lty=3, col="gray")#
abline(h=threshold,lwd=3,col="blue")#
mtext(c(expression(Upsilon1),expression(Psi)),side=c(2,4),line=3,las=1)#
par(old.par)
rep(1:2,2)
?factor
  y <- rnorm(100)
  x1 <- gl(2,50,100,labels=paste("c",1:2,sep=""))
  x2 <- factor(rep(1:4,25),labels=letters[1:4])
y
x1
x2
  y <- rnorm(100)
  x1 <- gl(2,50,100,labels=paste("c",1:2,sep=""))
  x2 <- factor(rep(1:4,25),labels=letters[1:4])
  y.means <- tapply(y,list(x1,x2),mean)
  y.sd <- tapply(y,list(x1,x2),sd)

  my.barplot <- function(data, err, ...) {
    tmp <- barplot(data, ...)
    if (length(err) != length(data))
        stop("la longueur de 'data' et 'err' ne correspond pas")
    for (i in 1:length(err))
        arrows(tmp[i],data[i]-err[i],tmp[i],data[i]+err[i],
	       code=3,angle=90,length=0.08)
  }

  my.barplot(y.means,y.sd,beside=T,ylab="Y",xlab="X2",
             ylim=c(0,26),names.arg=levels(x2),legend.text=levels(x1),
	     cex.axis=.7,cex.names=.7,cex.lab=.7)
 y <- rnorm(100,mean=20)
  x1 <- gl(2,50,100,labels=paste("c",1:2,sep=""))
  x2 <- factor(rep(1:4,25),labels=letters[1:4])
  y.means <- tapply(y,list(x1,x2),mean)
  y.sd <- tapply(y,list(x1,x2),sd)

  my.barplot <- function(data, err, ...) {
    tmp <- barplot(data, ...)
    if (length(err) != length(data))
        stop("la longueur de 'data' et 'err' ne correspond pas")
    for (i in 1:length(err))
        arrows(tmp[i],data[i]-err[i],tmp[i],data[i]+err[i],
	       code=3,angle=90,length=0.08)
  }

  my.barplot(y.means,y.sd,beside=T,ylab="Y",xlab="X2",
             ylim=c(0,26),names.arg=levels(x2),legend.text=levels(x1),
	     cex.axis=.7,cex.names=.7,cex.lab=.7)
  y <- c(rnorm(50,mean=20),rnorm(50,mean=15))
  x1 <- gl(2,50,100,labels=paste("c",1:2,sep=""))
  x2 <- factor(rep(1:4,25),labels=letters[1:4])
  y.means <- tapply(y,list(x1,x2),mean)
  y.sd <- tapply(y,list(x1,x2),sd)

  my.barplot <- function(data, err, ...) {
    tmp <- barplot(data, ...)
    if (length(err) != length(data))
        stop("la longueur de 'data' et 'err' ne correspond pas")
    for (i in 1:length(err))
        arrows(tmp[i],data[i]-err[i],tmp[i],data[i]+err[i],
	       code=3,angle=90,length=0.08)
  }

  my.barplot(y.means,y.sd,beside=T,ylab="Y",xlab="X2",
             ylim=c(0,26),names.arg=levels(x2),legend.text=levels(x1),
	     cex.axis=.7,cex.names=.7,cex.lab=.7)
  y <- c(rnorm(50,mean=20),rnorm(50,mean=15,sd=3))
  x1 <- gl(2,50,100,labels=paste("c",1:2,sep=""))
  x2 <- factor(rep(1:4,25),labels=letters[1:4])
  y.means <- tapply(y,list(x1,x2),mean)
  y.sd <- tapply(y,list(x1,x2),sd)

  my.barplot <- function(data, err, ...) {
    tmp <- barplot(data, ...)
    if (length(err) != length(data))
        stop("la longueur de 'data' et 'err' ne correspond pas")
    for (i in 1:length(err))
        arrows(tmp[i],data[i]-err[i],tmp[i],data[i]+err[i],
	       code=3,angle=90,length=0.08)
  }

  my.barplot(y.means,y.sd,beside=T,ylab="Y",xlab="X2",
             ylim=c(0,26),names.arg=levels(x2),legend.text=levels(x1),
	     cex.axis=.7,cex.names=.7,cex.lab=.7)
png("ex6.png")
  my.barplot(y.means,y.sd,beside=T,ylab="Y",xlab="X2",
             ylim=c(0,26),names.arg=levels(x2),legend.text=levels(x1),
	     cex.axis=.7,cex.names=.7,cex.lab=.7)
  a <- matrix(NA,nrow=len,ncol=2)
  a[,1] <- c(2,3,3,6,5,12,15,20)
  a[,2] <- c(1,4,2,3,9,10,30,35)
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  col <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=c(col.ciep[1],col.ciep[4]),las=1,xlab="Nb. associations",main="Langues représentées",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=c(col.ciep[1],col.ciep[4]),bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
  a <- matrix(NA,nrow=len,ncol=2)
  a[,1] <- c(2,3,3,6,5,12,15,20)
  a[,2] <- c(1,4,2,3,9,10,30,35)
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Nb. associations",main="Langues représentées",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
  a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- c(2,3,3,6,5,12,15,20)
  a[,2] <- c(1,4,2,3,9,10,30,35)
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Nb. associations",main="Langues représentées",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
  a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- rev(c(2,3,3,6,5,12,15,20))
  a[,2] <- rev(c(1,4,2,3,9,10,30,35))
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Nb. associations",main="Langues représentées",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
  a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- c(2,3,3,6,5,12,15,20)
  a[,2] <- c(1,4,2,3,9,10,30,35)
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(rev(a)),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Nb. associations",main="Langues représentées",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
 a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- c(2,3,3,6,5,12,15,20)
  a[,2] <- c(1,4,2,3,9,10,30,35)
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(rev(t(a)),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Nb. associations",main="Langues représentées",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
 a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- rev(c(2,3,3,6,5,12,15,20))
  a[,2] <- rev(c(1,4,2,3,9,10,30,35))
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Nb. associations",main="",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
  a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- rev(c(2,3,3,6,5,12,15,20))
  a[,2] <- rev(c(1,4,2,3,9,10,30,30))
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Effectifs",main="",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4)
  a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- rev(c(2,3,3,6,5,12,15,20))
  a[,2] <- rev(c(1,4,2,3,9,10,30,30))
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),rgb(180/255,210/255,244/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 20

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols,las=1,xlab="Effectifs",main="",xlim=c(0,max(a.margin)+x.offset))
  legend("topright",c("1","2"),pch=rep(19,2),col=cols,bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4,cex=.8)
  a <- matrix(NA,nrow=8,ncol=2)
  a[,1] <- rev(c(2,3,3,6,5,12,15,20))
  a[,2] <- rev(c(1,4,2,3,9,10,30,30))
  rownames(a) <- LETTERS[1:8]
  colnames(a) <- c("1","2")
  cols <- c(rgb(105/255,166/255,233/255),
            rgb(180/255,210/255,244/255),
	    rgb(0/255,78/255,162/255))

  a.prop <- round(a/sum(a)*100,2)
  a.margin <- apply(a,1,sum)
  x.offset <- 25

  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols[1:2],las=1,xlab="Effectif",main="",xlim=c(0,max(a.margin)+x.offset),border=cols[3])
  legend("topright",c("1","2"),pch=rep(19,2),col=cols[1:2],bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4,cex=.8)
png("ex7.png")
  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols[1:2],las=1,xlab="Effectif",main="",xlim=c(0,max(a.margin)+x.offset),border=cols[3])
  legend("topright",c("1","2"),pch=rep(19,2),col=cols[1:2],bty="n")
  labs <- paste(paste(as.character(a.prop[,1]),"%",sep=""),paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4,cex=.8)
  par(mar=c(5,6,4,2))
  bp <- barplot(t(a),names.arg=rownames(a),horiz=T,col=cols[1:2],
                las=1,xlab="Effectif",main="",xlim=c(0,max(a.margin)+x.offset),
                border=cols[3])
  legend("topright",c("1","2"),pch=rep(19,2),col=cols[1:2],bty="n")
  labs <- c(paste(as.character(a.prop[,1]),"%",sep=""),
                paste(as.character(a.prop[,2]),"%",sep=""),sep=" / ")
  text(a.margin,bp,labs,pos=4,cex=.8)
  a<-rnorm(100)
  b<-2*a+rnorm(100)
  c<-5*a+rnorm(100)+runif(100)*2
  pairs(cbind(a,b,c))
png("ex8.png")
pairs(cbind(a,b,c))
help.search("hexbin")
library(hexbin)
?hexbin
x <- rnorm(10000)#
y <- rnorm(10000)
plot(hexbin(x, y + x*(x+1)/4),#
     main = "(X, X(X+1)/4 + Y)  where X,Y ~ rnorm(10000)")
?plotmath
  plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1)/4,Y) ~~ X,Y iid ~ cal(N)")
  plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1)/4,Y) ~~ X,Y iid %~% bold(N)")
  plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1)/4,Y)))
  plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1),4)+Y)))
  plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1),4)%+%Y)))
 plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1),4) + Y))
 plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
     main = expression(frac(X %.% (X+1),4) + Y ~~ X,Y))
png("ex10.png")
  plot(hexbin(x, y + x*(x+1)/4), ylab="Y",
       main=expression(frac(X %.% (X+1),4) + Y))
?contourplot
?contour
library(survey)
?survey
help.search("survey")
data(api)#
dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)#
#
svyplot(api00~api99, design=dstrat, style="bubble")
?svyplot(api00~api99, design=dstrat, style="hex", xlab="1999 API",ylab="2000 API")
svyplot(api00~api99, design=dstrat, style="hex", xlab="1999 API",ylab="2000 API")
svyplot(api00~api99, design=dstrat, style="hexgray", xlab="1999 API",ylab="2000 API")
svyplot(api00~api99, design=dstrat, style="grayhex", xlab="1999 API",ylab="2000 API")
png("ex11.png")
svyplot(api00~api99, design=dstrat, style="bubble")
  par(mfrow=c(1,2))
  svyplot(api00~api99, design=dstrat, style="hex", xlab="1999 API",
          ylab="2000 API")
  svyplot(api00~api99, design=dstrat, style="grayhex",legend=0)
?layout
layout(matrix(1,2),1,2,byrow=T)
layout(matrix(1,2),1,2,byrow=T))
layout(matrix(c)(1,2),1,2,byrow=T))
layout(matrix(c(1,2),1,2,byrow=T))
layout.show()
svyplot(api00~api99, design=dstrat, style="hex", xlab="1999 API",#
        ylab="2000 API")
png("ex12.png")
svyplot(api00~api99, design=dstrat, style="hex", xlab="1999 API",
          ylab="2000 API")
png("ex13.png")
svyplot(api00~api99, design=dstrat, style="grayhex",legend=0)
library(ggplot)
library(ggplot2)
diamonds <- read.csv("http://had.co.nz/stat480/lectures/diamonds.csv")
d <- diamonds
qplot(price, data=d, type="histogram")
str()diamonds)
str(diamonds)
qplot(price, data=d, type="histogram", breaks=seq(0,20000, by=500))
ggfluctuation(table(d$cut, d$color))
?qplot
qplot(price, carat, data=diamonds)
qplot(carat, price, data=diamonds, colour=color)
png("ex14.png")
qplot(carat, price, data=diamonds, size=carat)
dev.off()