RHelp_gardenTrix

gardentrix.R

library(openxlsx)
library(readxl)
library(Hmisc)
library(tidyverse)

#write out the iris dataset
# write.xlsx(iris, "iris.xlsx") just to show you how

# read in a dataset from excel
iris2 <- read_excel("iris.xlsx") # this assumes it's in R's working directory (the one it boots up with)

glimpse(iris2) # let's take a look at the structure
# note each individual is on its own line, each "trait" is a column

ggplot(data = iris2, aes(x = Species, y = Sepal.Length, colour = Species)) + #set up what everything is for plot
	stat_summary(fun.data = "mean_cl_boot") # compute confidence interval using raw data and bootstrap mean, uses Hmisc package
	
ggsave("single_trait_plot.png") #save it out

#what if I want to plot all of the traits?
# we need to reshape the data further using tidyr::gather()

iris2 %>% 
	gather(data = ., key = Trait, value = Value, -Species) %>% #gather up the traits into a Trait column, put the numbers into the value column and keep species to the side
	ggplot(data = ., aes(x = Species, y = Value, colour = Species)) + 
		stat_summary(fun.data = "mean_cl_boot") +
				facet_wrap(~Trait, scales = "free_y", nrow = 2, strip.position = "bottom") # facet by Trait, 2 rows and put labels on the bottom

ggsave("faceted_plot.png") #save it out