DEPARTMENT OF BIOSTATISTICS UNIVERSITY OF COPENHAGEN. Graphics. Compact R for the DANTRIP team. Klaus K. Holst

Transcription

1 Graphics Compact R for the DANTRIP team Klaus K. Holst

2 The R Graphics system R has a very flexible and powerful graphics system Basic plot routine: plot(x,y,...) low-level routines: lines, points, text, title, legend,... Example of high-level routines: qqnorm, hist, boxplot,... Many classes have attached plot-method, e.g.: plot(density(iris$sepal.length))

3 Graphics methods plot(density(iris$sepal.length))

4 Iris data For illustration purposes we are using the Anderson s Iris flower data set consisting of measurements of sepal length and width and petal length and with of 50 flowers of specie iris setosa, versicolor and virginica.

5 Iris data pairs(iris, col=as.numeric(iris$species))

6 Graphics methods (m1 <- methods("plot")) [1] plot.holtwinters* plot.tukeyhsd plot.acf* [4] plot.correspondence* plot.data.frame* plot.decompos [7] plot.default plot.dendrogram* plot.density [10] plot.ecdf plot.factor* plot.formula* [13] plot.function plot.hclust* plot.histogra [16] plot.isoreg* plot.lda* plot.lm [19] plot.mca* plot.medpolish* plot.mlm [22] plot.ppr* plot.prcomp* plot.princomp [25] plot.profile* plot.profile.nls* plot.ridgelm* [28] plot.shingle* plot.spec plot.stepfun [31] plot.stl* plot.table* plot.trellis* [34] plot.ts plot.tskernel* Non-visible functions are asterisked

7 The R Graphics system Traditional system Lattice Grid (library(grid), see R Graphics, by Paul Murrell) paul/rg2e/ ggplot2 (Grammar of Graphics) Limited support for interactive graphics

8 Lattice Library of high-level plot functions including scattter-plots, density plots, qq-plots, level plots,... Particularly well suited to visualize longitudinal and grouped data. k <- 10 n <- 20 id <- y <- x <- c() set.seed(1) for (i in seq(n)) { x0 <- seq(k)+runif(k,0,0.5) u <- rnorm(1,sd=1.5) x <- c(x,x0) id <- c(id,rep(i,k)) y <- c(y,rnorm(k,u+x0,sd=0.8)) } z <- as.factor(rep(c(0,1),each=k*n/2)) d <- data.frame(y=y,x=x,id=id,z=z)

9 Lattice print(xyplot(y ~ x, group=id, type="l", data=d, col="darkblu

10 Lattice print(xyplot(y ~ x z, group=id, type="l", data=d))

11 Lattice xyplot(y ~ x id, type="l", data=d)

12 ggplot2 Implementation of Grammar of Graphics library(ggplot2) p1 <- qplot(sepal.length,sepal.width,data=iris,colour=species) p1

13 ggplot2 p2 <- p1 + xlab(expression(eta)) + ylab(expression(phi(eta))) p2 <- p2 + opts(axis.title.x=theme_text(size=15,vjust=0.5), axis.title.y=theme_text(size=15,vjust=0.5,angle=90)) p2

14 ggplot2 p3 <- p2 + stat_smooth(span=0.75,se=true,colour="darkblue") p3+geom_point(shape=1,size=3)

15 3D graphics, surface plots x <- seq(0,3,by=.05) z <- outer(x,x,fun=function(x,y) sin(x*y)+x^2) contour(x,x,z)

16 3D graphics, contour plots filled.contour(x,x,z)

17 3D graphics, images image(z,col=heat.colors(50))

18 3D graphics, surface persp(x,x,z,theta=-40,phi=30,col="lightgray")

19 3D graphics, scatter plots library(scatterplot3d) with(iris, scatterplot3d(sepal.length, Petal.Length, Petal.Width,color=as.numeric(Species)))

20 3D graphics, rgl Interactive plots via rgl library(rgl) persp3d(x,x,z,col="orange") with(iris, plot3d(cbind(sepal.length, Petal.Length, Petal.Width), col=as.numeric(species), type="s",radius=0.07))

21 Interactive graphics A few third party libraries are available which implements some support for interacting with plots such as brushing Iplots rggobi playwith rpanel rgl, misc3d all available on CRAN

22 Identifying points, brushing source("color.r") plot(sepal.length ~ Petal.Length, data=iris) idp <- with(iris, Id(Petal.Length,Sepal.Length)) Text("My label")

23 Mathematical annotation x <- seq(0,2, by=0.001) f1 <- sqrt(x) f2 <- x^2 plot(x, f1, type= l, lty=1, col="red", ylab="f(x)") lines(x, f2, lty=2, col="blue") legend("bottomright", legend=c(expression(f[1](x)==sqrt(x)), expression(phi(x)==x^2) ), col=c("red","blue"), lty=c(1,2)) title(expression(sum(delta[i],i==1,n)==integral(f(x)*dx,a,b)

24 Mathematical annotation

25 Large data load("prt.rda") str(prt) head(prt) prt <- prt[order(prt$id),] prt$twinnum <- unlist(lapply(table(prt$id),seq)) prtwide <- reshape(prt,direction="wide", idvar=c("id","zyg","country"),timevar="twinnum") head(prt) data.frame : obs. of 6 variables: $ country: Factor w/ 4 levels "Denmark","Finland",..: $ time : num $ status : int $ zyg : Factor w/ 2 levels "DZ","MZ": $ id : int $ cancer : num country time status zyg id cancer

26 Large data plot(time.1~time.2,prtwide)

27 Large data plot(time.1~time.2,prtwide,pch=16,cex=0.5)

28 Large data library(hexbin) hp <- with(prtwide, hexbin(time.1,time.2)) plot(hp)

29 Large data plot(hp, style="centroids")

30 Large data cols <- c(rgb(0.5,0,0,0.1),rgb(0,0,0.5,0.1)) plot(time.1~time.2,prtwide,pch=16,cex=1, col=cols[as.numeric(prtwide$zyg)])

31 Colors and transparency The Col function from color.r can add transparency to a named color Col("blue",0.2) To select a color with the mouse you can call color(1)

32 Colors and transparency x <- seq(0,0.75,by=0.01) y1 <- log(x+1) y2 <- x^2 xx <- c(x,rev(x)) yy <- c(y1,rev(y2)) plot(xx,yy, type="n") polygon(xx,yy, col=col("blue",0.2)) polygon(xx,rev(yy)+0.1, col=col("red",0.2))

33 Colors and transparency

34 Practicals: transparent confidence bands 1 Fit a linear regression model to the iris data with Sepal.Length as the outcome and Sepal.Width as the covariate. Include the interaction with Species and assess the statistical significance of the interaction using a Likelihood Ratio Test or Wald test. 2 Make a scatter-plot of the two continuous variables (colored by Species) and add the estimated regression lines with transparent 95% confidence limits (in matching colors).