############################################################################################
data=read.delim("Supplementary data-ultrastructure.txt", header=T)

taxon=data[,"Taxon"]
length.2=data[,"CS_L"]
width.2=data[,"CS_W"]
length=ifelse(width.2>length.2,width.2,length.2)
width=ifelse(width.2<length.2, width.2, length.2)
preservation=data[,"Preservation"]
source=data[,"Source"]
bed=data[,"Sample"]
section=data[,"Section"]


layout(matrix(c(1,2,3,4,4,4,5,5,5,6,6,6), ncol=6, byrow=TRUE))
par(mar=c(4,4,2,0))
out1=boxplot(length.2[taxon=="praetintinnopsella"  & source=="SEM"],
length.2[taxon=="crassicollaria"  & source=="SEM"],length.2[taxon=="calpionella"  & source=="SEM"], 
main="", ylab="Length (um)", names=c("Praetintinnopsella","Crassicollaria","Calpionella"),
las=2, range=0, frame=F, cex=1.2, log="y", ylim=c(0.25,10), col=c("gray31","gray61","white"))

out2=boxplot(width.2[taxon=="praetintinnopsella"  & source=="SEM"],
width.2[taxon=="crassicollaria"  & source=="SEM"],width.2[taxon=="calpionella"  & source=="SEM"], 
main="", ylab="Width (um)", names=c("Praetintinnopsella","Crassicollaria","Calpionella"),
las=2, range=0, frame=F, cex=1.2, log="y", ylim=c(0.25,10), col=c("gray31","gray61","white"))

ratio=length.2/width.2
out3=boxplot(ratio[taxon=="praetintinnopsella"  & source=="SEM"],
ratio[taxon=="crassicollaria"  & source=="SEM"],ratio[taxon=="calpionella"  & source=="SEM"], 
main="", ylab="Length/Width ratio", names=c("Praetintinnopsella","Crassicollaria","Calpionella"),
las=2, range=0, frame=F, cex=1.2, log="", col=c("gray31","gray61","white"))

plot(length.2, width.2, xlim=c(0.5,15), ylim=c(0.25,10),
xlab="Crystal length (um)", ylab="Crystal width (um)", type="n", frame=F, log="xy")
points(length.2[taxon=="praetintinnopsella"  & source=="SEM"], width.2[taxon=="praetintinnopsella"  & source=="SEM"], pch=21, bg="gray31")
points(length.2[taxon=="crassicollaria"  & source=="SEM"], width.2[taxon=="crassicollaria"  & source=="SEM"], pch=21, bg="gray61")
points(length.2[taxon=="calpionella"  & source=="SEM"], width.2[taxon=="calpionella"  & source=="SEM"], pch=21, bg="white")
legend(x="topleft", legend=c("Praetintinnopsella","Crassicollaria","Calpionella"), 
pch=c(21,21,21),  pt.bg=c("gray31","gray61","white"), cex=1.3, bty="n")

out1$stats[3,]
out2$stats[3,]
out3$stats[3,]
