Dietary Composition

Based on data from The Ratio of Macronutrients, Not Caloric Intake, Dictates Cardiometabolic Health, Aging, and Longevity in Ad Libitum-Fed Mice
I have downloaded PDFs of both the paper and the supplemental material (as well as an xslx spreadsheet).

Use of Trilinear/Ternary plot suggested by (looks like this is done using the klaR package):

Diet details

Survival by diet

Notice that the highest median lifespan is for the High energy content version of diet 9 (42P/29C/29F).

Not working 8/9/14. Why? Turned off eval for now.

library(ggtern)

# survival_all <- read.csv("C:/Users/rseiter/Documents/Health/Nutrition/The Ratio of Macronutrients, Not Caloric Intake/survival.csv")
survival_all <- read.csv("~/Health/Nutrition/The Ratio of Macronutrients, Not Caloric Intake/survival.csv")
survival_all$Protein <- as.numeric(survival_all$Protein)
survival_all$Energy <- as.numeric(survival_all$Energy)

energy <- "HIGH"
survival <- subset(survival_all, Energy.Density==energy)
output <- ggtern(data=survival,aes(x=Protein,y=Carb,z=Fat),aes(x,y,z)) + 
  stat_density2d(geom="polygon",
                 n=400,
                 aes(fill=..level..,
                 weight=survival$Median.lifespan,
                 alpha=abs(..level..)),
                 binwidth=100) + 
#  facet_grid(survival$Energy.Density ~ .) + # Why failing?
  geom_density2d(aes(weight=survival$Median.lifespan,color=..level..),
                 n=400,
                 binwidth=100) +
  geom_point(aes(fill=survival$Median.lifespan),color="black",size=6,shape=21) + 
  geom_text(aes(label=Diet),size=4) + 
#  facet_wrap(survival$Energy.Density ~ ) + # Why failing?
  scale_fill_gradient(low="yellow",high="red") + 
  scale_color_gradient(low="yellow",high="red") + 
  theme_rgbw() + 
  percent_custom("%")   + #make ternary scales on custom %
  theme(legend.justification=c(0,1), legend.position=c(0,1)) + 
  guides(fill = guide_colorbar(order=1),
         alpha= guide_legend(order=2),
         color="none") + 
  labs(  title= paste("Median Lifespan by Dietary Composition -", energy, "Energy"),
         fill = "Median Lifespan", alpha="Median Lifespan") # Why fill AND alpha?

# Focus on our space.  Had to change/fix rounding to make this work right.
# Why problem with generating contours?
# I actually find the full plot more informative.
#   last_plot() + coord_tern(Tlim=c(.2,.75),Llim=c(.05,0.6),Rlim=c(.2,0.75)) +
#   labs(title=paste("Refocused Median Lifespan by Dietary Composition -", energy, "Energy"))

summary(output)
output

Why is rendering failing for this?

plotMedianLifespan <- function (survival_all, energy) {
  survival <- subset(survival_all, Energy.Density==energy)
  output <- ggtern(data=survival,aes(x=Protein,y=Carb,z=Fat),aes(x,y,z)) + 
    stat_density2d(geom="polygon",
                   n=400,
                   aes(fill=..level..,
                   weight=survival$Median.lifespan,
                   alpha=abs(..level..)),
                   binwidth=100) + 
  #  facet_grid(survival$Energy.Density ~ .) + # Why failing?
    geom_density2d(aes(weight=survival$Median.lifespan,color=..level..),
                   n=400,
                   binwidth=100) +
    geom_point(aes(fill=survival$Median.lifespan),color="black",size=6,shape=21) + 
    geom_text(aes(label=Diet),size=4) + 
  #  facet_wrap(survival$Energy.Density ~ ) + # Why failing?
    scale_fill_gradient(low="yellow",high="red") + 
    scale_color_gradient(low="yellow",high="red") + 
    theme_rgbw() + 
    percent_custom("%")   + #make ternary scales on custom %
    theme(legend.justification=c(0,1), legend.position=c(0,1)) + 
    guides(fill = guide_colorbar(order=1),
           alpha= guide_legend(order=2),
           color="none") + 
    labs(  title= paste("Median Lifespan by Dietary Composition -", energy, "Energy"),
           fill = "Median Lifespan", alpha="Median Lifespan") # Why fill AND alpha?
  
  # Focus on our space.  Had to change/fix rounding to make this work right.
  # Why problem with generating contours?
  # I actually find the full plot more informative.
#   last_plot() + coord_tern(Tlim=c(.2,.75),Llim=c(.05,0.6),Rlim=c(.2,0.75)) +
#   labs(title=paste("Refocused Median Lifespan by Dietary Composition -", energy, "Energy"))

  # Render here directly?
  (output)

  return(output)
}

# This would be better done with faceting
for (energy in c("LOW", "MEDIUM", "HIGH")) {
  print(energy)
  output <- plotMedianLifespan(survival_all, energy)
  summary(output)
  # Render
  output
}