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July 12, 2016 17:02
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A boxplot replacement that I call the "Jelly Bean Plot".
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jelly.beans <- function(data, brewerset = "Set1", cols = brewer.pal(length(data),brewerset), | |
diffs = rep(NA,length(data)), notches = FALSE, | |
xlab = NA, ylab = NA, las = rep(0,2), bean.width = c(3,8,3,1,2), ...) { | |
require(RColorBrewer) | |
# data = list(grp1=vector(),grp2=vector(),grp3=vector()) | |
# bean.width = c(0.95-lines,0.5-lines,median-line,grid-line) | |
# diffs = c("A", "A", "B") eg to present TukeyHSD values | |
do.call(rbind,lapply(1:length(data),function(i) c(i,data[[i]]))) | |
num.grps <- length(data) | |
grp.names <- names(data) | |
mu <- lapply(data,mean,na.rm=TRUE) | |
hpd <- lapply(data,quantile,probs=c(0.025,0.25,0.5,0.75,0.975),na.rm=TRUE) | |
yrange <- range(hpd) | |
plot(1,type="n",xlim=c(0,num.grps+1),ylim=yrange,axes=FALSE,xlab=NA,ylab=NA,...) | |
if (notches) { | |
for (i in 1:num.grps) { | |
iqr <- hpd[[i]][3]+c(-1,1)*(hpd[[i]][4]-hpd[[i]][2])*1.58/sqrt(length(data[[i]])) | |
rect(0.5,iqr[1],num.grps+0.5,iqr[2],col=paste(cols[i],"33",sep=""),border=NA) | |
lines(c(0.5,num.grps+0.5),rep(iqr[1],2),col=cols[i],lty=2) | |
lines(c(0.5,num.grps+0.5),rep(iqr[2],2),col=cols[i],lty=2) | |
} | |
} | |
for (i in 1:num.grps) { | |
lines(c(i,i),yrange,col=rgb(.5,.5,.5),lwd=bean.width[4]) | |
lines(c(i,i),hpd[[i]][c(1,5)],col=cols[i],lwd=bean.width[1]) | |
lines(c(i,i),hpd[[i]][c(2,4)],col=cols[i],lwd=bean.width[2]) | |
if (notches) { | |
lines(i+c(-.2,.2),rep(hpd[[i]][3],2),col=cols[i],lwd=bean.width[3]*1.1) | |
} | |
lines(i+c(-.2,.2),rep(hpd[[i]][3],2),col="white",lwd=bean.width[3]) | |
} | |
axis.at <- 1:num.grps | |
axis(1,at=axis.at,labels=grp.names,las=1,lwd=0,pos=yrange[1],cex.axis=.8) | |
axis(3,at=axis.at,labels=diffs,las=1,lwd=0,pos=yrange[2],cex.axis=.8) | |
x.tics <- axTicks(2) | |
lines(c(0,0),c(min(yrange,x.tics),max(yrange,x.tics))) | |
axis(2,at=x.tics,pos=0,lwd=0,lwd.ticks=1,las=1,tcl=-0.3) | |
if (! is.na(xlab)) mtext(xlab,side=1,line=2,las=las[1]) | |
if (! is.na(ylab)) mtext(ylab,side=2,line=2,las=las[2]) | |
} | |
library(multcompView) | |
data <- lapply(1:4,rnorm,n=20,sd=1) | |
names(data) <- c("Monkey","Possum","Armadillo","Tardigrade") | |
data.df <- data.frame(do.call(rbind,lapply(1:4,function(i) | |
cbind(Animal=i,Awesomeness=data[[i]])))) | |
data.df$Animal <- factor(data.df$Animal) | |
mo <- aov(Awesomeness~Animal,data=data.df) | |
mo.hsd <- TukeyHSD(mo) | |
diffs <- rev(multcompLetters2(Awesomeness~Animal,mo.hsd$Animal[,"p adj"], | |
data.df,reversed=TRUE)$Letters) | |
pdf(file="jellyBeans.pdf",width=12,height=6) | |
par(mfrow=c(1,2)) | |
jelly.beans(data,ylab="Awesomeness",xlab="Animal",notches=FALSE, | |
las=c(1,0),bean.width=c(10,20,10,1,5),diffs=diffs) | |
jelly.beans(data,ylab="Awesomeness",xlab="Animal",notches=TRUE, | |
las=c(1,0),bean.width=c(10,20,10,1,5),diffs=diffs) | |
dev.off() |
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which version of R did you develop this in? I am having trouble with the
multcompView
package.