#load data & libaries
library(smatr)

# rm(list=ls())

# data4 <- read.csv('Trait data, 5-2-2014.csv', header = T, sep = ",") 
data4 <- read.csv('Trait data.csv', header = T, sep = ",") 

# _______________________ PLOTTING _____________________________________________###
 
 cool_dry <- subset (data4, climate.description == "Temperate_Dry", select = colnames(data4))
 warm_wet <- subset (data4, climate.description == "Subtropical_Wet", select = colnames(data4))
 hot_dry <- subset (data4, climate.description == "Tropical_Monsoonal", select = colnames(data4))
 warm_arid <- subset (data4, climate.description == "Subtropical_Arid", select = colnames(data4))
 warm_dry <- subset (data4, climate.description == "Subtropical_Dry", select = colnames(data4))
  
 
# ______________Fig 1 (leaf size ~ total_flow_petiole)__________________________________________## 

## TURN ON IF SAVING TO FILE
 tiff(file="petiole_K vs LS2.tiff", height=4.1, width=4.5, units="in", res=200) 
# pdf("petiole_K vs LS.pdf", height=4.1, width=4.5)
#postscript("myplot.eps", horizontal = FALSE, onefile = FALSE, paper = "special", height = 4.5, width = 5) 

par(mfrow=c(1,1),  oma=c(0.2, 0.5, 0.2, 0.2), mai=c(0.7, 0.7, 0.3, 0.3), mgp=c(2, 0.5, 0))
# par(mfrow=c(1,1),  oma=c(0.5, 0.5, 0.5, 0.5), mai=c(1, 0.9, 0.5, 0.5), mgp=c(2.2,0.5,0))

  
 plot(data4[,"total_flow_pet..kg.m.s.Mpa."]*1000000, data4[,"leaf.size..cm2."],axes=FALSE, pch=19,
      cex.lab=1.2, cex=1.5, xlim=c(0.0003, 2), ylim=c(0.09, 100), log="xy", col="white",   
      xlab=expression("petiole K (mg  " *  m^-1 *" "* s^-1*" "* MPa^-1 * ")"),
      ylab=expression("leaf size (" *  cm^2 * ")"))
 labels <- c(0.001, 0.01, 0.1, 1)
 axis(1, tick=TRUE, line=0, tck=0.025, cex.axis=0.75, at=labels)
 axis(2, tick=TRUE, line=0, las=2, tck=0.025, cex.axis=0.75)
 box(bty="l")
 
 points(cool_dry[,"total_flow_pet..kg.m.s.Mpa."]*1000000, cool_dry[,"leaf.size..cm2."], pch=0, cex=1.2, col="blue",lwd=2)
 points(warm_wet[,"total_flow_pet..kg.m.s.Mpa."]*1000000, warm_wet[,"leaf.size..cm2."], pch=1, cex=1.2, col="darkorchid3",lwd=2)
 points(hot_dry[,"total_flow_pet..kg.m.s.Mpa."]*1000000, hot_dry[,"leaf.size..cm2."], pch=2, cex=1.2, col="red",lwd=2)
 points(warm_arid[,"total_flow_pet..kg.m.s.Mpa."]*1000000, warm_arid[,"leaf.size..cm2."], pch=3, cex=1.2, col="darkorchid3",lwd=2)
 points(warm_dry[,"total_flow_pet..kg.m.s.Mpa."]*1000000, warm_dry[,"leaf.size..cm2."], pch=5, cex=1.2, col="darkorchid3",lwd=2)
 
 OLS1=line.cis(log10(data4[,"leaf.size..cm2."]), log10(data4[,"total_flow_pet..kg.m.s.Mpa."]*1000000), method="SMA")
 curve(10^((log10(x)*(OLS1[2,1])+(OLS1[1,1]))), lwd=1, add=T, xlim=c(0.0003, 2))
 
 # 1:1 direct proportionality line 
 curve((x)*(500), lwd=1, lty=2, add=T, xlim=c(0.0003, 2), col="red")
 
 #  title(main = expression("petiole ~ branch"), sub = NULL, xlab = NULL, ylab = NULL,
 #  line = NA, outer = FALSE, cex.main=1.7) 
 
 lm <- lm(log10(data4[,"total_flow_pet..kg.m.s.Mpa."]*1000000) ~ log10(data4[,"leaf.size..cm2."])); summary(lm)
 
text <- expression(r^2 * " = 0.84, p < 0.001") 
legend("topleft", text, bty="n", cex=1)


 
# ______________Fig 1, panel 2 (variance partitioning - Ks vs x-sec area bargraph)___________## 

par(fig = c(0.67, 0.89, 0.20, 0.48), new = TRUE)
par(mgp=c(2.7,0.2,0))
par(mar = c(1.2, 0, 1.5, 0))

var_Ks <- c(46.6, 53.4)
barplot(var_Ks, cex.axis=0.5, tck=FALSE)
box(lty=1, bty="l")

axis(2, tick=TRUE, line=0, labels=FALSE, tck=-0.05)  
axis(1, tick=FALSE, labels=FALSE, cex.axis=0.5) 

text(0.75, -7, cex=0.6, labels=expression(K[X]), xpd=TRUE)
text(1.95, -7, cex=0.6, labels="xylem", xpd=TRUE)
text(1.95, -16, cex=0.6, labels="area", xpd=TRUE)
text(1.2, 69, cex=0.6, labels="explained", xpd=TRUE)
text(1.2, 59, cex=0.6, labels="variance (%)", xpd=TRUE)

# TURN ON/OFF
 dev.off()