Trait Analysis

Goal

Analyze the relative abundance of a bunch of traits

pcks <- c("magrittr", "plyr", "ggplot2")
a <- sapply(pcks, require, character = TRUE)

There is a data frame that looks like this:

load("../data/trait.dataframe.rda")
str(trait.dataframe)

## 'data.frame':    40258 obs. of  6 variables:
##  $ Person  : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ Transect: Factor w/ 3 levels "ax","ay","fx": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Location: int  1 2 3 4 5 6 7 8 9 10 ...
##  $ Trait   : Factor w/ 29 levels "Carbon_Source_General",..: 1 1 1 1 1 1 1 1 1 1 ...
##  $ Variable: chr  "heterotrophic" "heterotrophic" "heterotrophic" "heterotrophic" ...
##  $ Value   : num  0.195 0.805 0.743 0.902 0.316 ...

I am not sure what its provenance is. I assume the number under Value represents the total relative abundance of that particular trait at a location, but honestly I have no idea - I’ve looked through all of my code and nowhere found code that I’ve written to create it, though it looks like something I would have created.

Trait abundance plots

Below, a whole bunch of plots of the different traits across the different locations across the different transects:

traits <- levels(trait.dataframe$Trait)

require(ggthemes)
for(t in traits){
  cat(paste0("### ", t, "\r\r"))
  p1 <- ggplot(trait.dataframe %>% subset(Trait == t), 
         aes(Location, Value, col = Variable)) + facet_wrap(.~Transect) + geom_point() + theme_few() 
  p2 <- ggplot(trait.dataframe %>% subset(Trait == t), 
         aes(Variable, Value, col = Variable)) + facet_wrap(.~Transect) + geom_boxplot() + theme_few()
  p3 <- ggplot(trait.dataframe %>% subset(Trait == t), 
         aes(Variable, Value, col = Variable)) + facet_wrap(.~Transect) + geom_boxplot() + theme_few() + scale_y_continuous(trans='log10')

  print(p1)
  print(p2)
  print(p3)
  cat("\r\r")
}