################################## # Advanced graphing commands ##################################

Transcription

1 ################################## # Advanced graphing commands ################################## trillium <- read.table(" attach( trillium ) # Some detailed control over graphs par(mfrow=c(1,1)) boxplot( stem ~ site, range=0 ) # range=0 has whiskers stretch to extremes # default is range=1.5, whiskers out 1.5 IQR from box boxplot( stem ~ site, xlab="site",ylab="stem length (cm)" ) axis( side=4, at=(2.54*(1:3)), labels=1:3, tck=0.01, mgp=c(-1,0,-0.1)) # help( axis ) # help( par ) # tck is par command for tick lengths and direction # mgp is par command to determine axis title, labels, and line location mtext("inches",side=4,line=.7,font=2, col="magenta") # help( mtext ) # font=2 is bold font, line is location of margin text str(colors()) chr [1:657] "white" "aliceblue" "antiquewhite" "antiquewhite1"...colors() 1

2 stem length (cm) inches site boxplot( stem ~ site, axes=f ) axis( side=1, at=1:4,labels=1:4, tck=0, lty=0) axis( side=2, at=1:9,labels=1:9 ) mtext("site",side=1) mtext("stem length (cm)", side=2, line=2.2 ) axis( side=2, at=c(2,4,6,8),tck=1, lty=3, lwd=.2) # tck=1 draws grid lines across graph, see help(par) Stem length (cm) Site

3 # Controlling multiple graphs on a page without mfrow() layout( rbind( c(1,2), c(3,4) ), height=c(1,2), width=c(1.5,1)) hist(stem) hist(leaf) plot(leaf, stem, pty="s"); abline( lm( stem ~ leaf ) ) title( main=expression( beta[0] + beta[1]*leaf ) ) plot(stem, leaf); fit <- lm( leaf ~ stem ) abline( fit ) title( main=substitute( paste(beta[0]==beta0," and ",beta[1]==beta1), list(beta0=signif(fit$coef[1],3),beta1=signif(fit$coef[2],3)) ) ) Frequency Histogram of stem Frequency Histogram of stem leaf 0 1 leaf and stem leaf leaf stem 3

4 layout( rbind( c(1,1,2,2),c(0,3,3,0) ), width=c(1,2,2,1), height=c(3,4)) pie( table( flower) ) boxplot( stem~flower ) plot(leaf,stem, xaxt="n" ) # no x axis labels title("not a true Stem-and-leaf plot" ) layout( 1 ) mtext(side=3,"three graphs", line=2.3, cex=1.5 ) Three graphs s w p p s w Not a true Stem-and-leaf plo stem leaf 4

5 x <- seq(from=-pi,to=pi,length=10) y <- seq(from=0,to=(2*pi),length=10) xy.grid <- expand.grid(x=x,y=y) dim(xy.grid) z <- sin(xy.grid[,1])+ cos(xy.grid[,2]) zmat <- matrix(z,ncol=10,byrow=f) layout(rbind(c(1,2),c(3,4))) contour(x,y,zmat) persp(x,y,zmat) x <- seq(from=-pi,to=pi,length=50) y <- seq(from=0,to=(2*pi),length=50) xy.grid <- expand.grid(x=x,y=y) dim(xy.grid) z <- sin(xy.grid[,1])+ cos(xy.grid[,2]) zmat <- matrix(z,ncol=50,byrow=f) contour(x,y,zmat,nlevels=15) persp(x,y,zmat, theta=40, phi=40, r=4) # theta and phi control angle of view # r controls distance from box 5

6 zmat y zmat y x zmat x y layout(1) persp(x,y,zmat, theta=40, phi=40, r=4) layout(c(1,2),respect=t) # respect=t forces aspect ratio to be the same image(x,y,zmat) plot( runif(100), runif(100) ) x 6

7 ########################### # Trellis plots # Go online and get package "lattice" # commercial package S-Plus beat R to the library name "trellis" library( lattice ) candy <- read.table(" attach(candy) Change <- After - Before xyplot( After ~ Before Treatment ) # obvious correlation nothing After cool hot Before xyplot( Change ~ Before Treatment ) # colder people heat up more nothing Change cool 0-1 hot Before 7

8 cloud( Change ~ After * Before Treatment ) # hard to interpret nothing Change Before After cool hot Change Change Before After Before After coplot( After~Before Change, panel=panel.smooth ) Given : Change After Before 8

9 # condition on one continuous variable and one categorical coplot( After ~ Before Change*Treatment, panel=panel.smooth) Given : Change cool After hot nothing Given : Treatment Before 9

10 ############## ## Bird data ############ birds <- read.table(" skip=15, header=t) names( birds ) attach(birds) coplot( wt ~ tl kl, panel=panel.smooth ) Given : kl wt tl # condition on two continuous variables coplot( wt ~ tl kl * bh, panel=panel.smooth) Given : kl wt Given : bh tl 10

11 #install ggplot2 package and load library(ggplot2) # See # 2176_ fc524dc0bc2a140573da38bb.html > str(diamonds) 'data.frame': obs. of 10 variables: $ carat : num $ cut : Ord.factor w/ 5 levels "Fair"<"Good"<..: $ color : Ord.factor w/ 7 levels "D"<"E"<"F"<"G"<..: $ clarity: Ord.factor w/ 8 levels "I1"<"SI2"<"SI1"<..: $ depth : num $ table : num $ price : int $ x : num $ y : num $ z : num > head(diamonds) carat cut color clarity depth table price x y z Ideal E SI Premium E SI Good E VS Premium I VS Good J SI Very Good J VVS > > qplot(carat, price, colour=clarity, alpha=i(1/3), size=depth, data=diamonds) > > qplot(x=color,y=price,geom="boxplot",data=diamonds) > > qplot(x=carat,y=price,colour=clarity,facets=~cut,data=diamonds) > > qplot(x=carat,y=price,colour=clarity,facets=color~cut,data=diamonds) 11

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15 ################################## # Advanced graphing commands ################################## trillium <- read.table(" ip=9) # Some detailed control over graphs par(mfrow=c(1,1)) boxplot( stem ~ site, range=0 ) # range=0 has whiskers stretch to extremes # default is range=1.5, whiskers out 1.5 IQR from box boxplot( stem ~ site, xlab="site",ylab="stem length (cm)" ) axis( side=4, at=(2.54*(1:3)), labels=1:3, tck=0.01, mgp=c(-1,0,-0.1)) # help( axis ) # help( par ) # tck is par command for tick lengths and direction # mgp is par command to determine axis title, labels, and line location 15

16 mtext("inches",side=4,line=.7,font=2, col="magenta") # help( mtext ) # font=2 is bold font, line is location of margin text colors() boxplot( stem ~ site, axes=f ) axis( side=1, at=1:4,labels=1:4, tck=0, lty=0) axis( side=2, at=1:9,labels=1:9 ) mtext("site",side=1) mtext("stem length (cm)", side=2, line=2.2 ) axis( side=2, at=c(2,4,6,8),tck=1, lty=3, lwd=.2) # tck=1 draws grid lines across graph, see help(par) # Controlling multiple graphs on a page without mfrow() layout( rbind( c(1,2), c(3,4) ), height=c(1,2), width=c(1.5,1)) hist(stem) hist(leaf) plot(leaf, stem, pty="s"); abline( lm( stem ~ leaf ) ) title( main=expression( beta[0] + beta[1]*leaf ) ) plot(stem, leaf); fit <- lm( leaf ~ stem ) abline( fit ) title( main=substitute( paste(beta[0]==beta0," and ",beta[1]==beta1), list(beta0=signif(fit$coef[1],3),beta1=signif(fit$coef[2],3)) ) ) layout( rbind( c(1,1,2,2),c(0,3,3,0) ), width=c(1,2,2,1), height=c(3,4)) pie( table( flower) ) boxplot( stem~flower ) plot(leaf,stem, xaxt="n" ) # no x axis labels title("not a true Stem-and-leaf plot" ) layout( 1 ) mtext(side=3,"three graphs", line=2.3, cex=1.5 ) x <- seq(from=-pi,to=pi,length=10) y <- seq(from=0,to=(2*pi),length=10) xy.grid <- expand.grid(x=x,y=y) dim(xy.grid) z <- sin(xy.grid[,1])+ cos(xy.grid[,2]) zmat <- matrix(z,ncol=10,byrow=f) layout(rbind(c(1,2),c(3,4))) contour(x,y,zmat) persp(x,y,zmat) x <- seq(from=-pi,to=pi,length=50) y <- seq(from=0,to=(2*pi),length=50) xy.grid <- expand.grid(x=x,y=y) dim(xy.grid) z <- sin(xy.grid[,1])+ cos(xy.grid[,2]) zmat <- matrix(z,ncol=50,byrow=f) contour(x,y,zmat,nlevels=15) persp(x,y,zmat, theta=40, phi=40, r=4) 16

17 # theta and phi control angle of view # r controls distance from box layout(1) persp(x,y,zmat, theta=40, phi=40, r=4) layout(c(1,2),respect=t) # respect=t forces aspect ratio to be the same image(x,y,zmat) plot( runif(100), runif(100) ) ########################### # Trellis plots # Go online and get package "lattice" # commercial package S-Plus beat R to the library name "trellis" library( lattice ) candy <- read.table(" der=t) attach(candy) Change <- After - Before xyplot( After ~ Before Treatment ) # obvious correlation xyplot( Change ~ Before Treatment ) # colder people heat up more cloud( Change ~ After * Before Treatment ) # hard to interpret coplot( After~Before Change, panel=panel.smooth ) # condition on one continuous variable and one categorical coplot( After ~ Before Change*Treatment, panel=panel.smooth) ############## ## Bird data ############ birds <- read.table(" skip=15, header=t) names( birds ) attach(birds) coplot( wt ~ tl kl, panel=panel.smooth ) # condition on two continuous variables coplot( wt ~ tl kl * bh, panel=panel.smooth) #install ggplot2 package and load library(ggplot2) # See # 2176_ fc524dc0bc2a140573da38bb.html str(diamonds) 17

18 head(diamonds) qplot(carat, price, colour=clarity, alpha=i(1/3), size=depth, data=diamonds) qplot(x=color,y=price,geom="boxplot",data=diamonds) qplot(x=carat,y=price,colour=clarity,facets=~cut,data=diamonds) qplot(x=carat,y=price,colour=clarity,facets=color~cut,data=diamonds) 18