annotate r squared to ggplot by using facet_wrap

Question

I just joined the community and looking forward to get some help for the data analysis for my master thesis.

At the moment I have the following problem:

I plotted 42 varieties with ggplot by using facet_wrap:

`ggplot(sumfvvar,aes(x=TemperaturCmean,y=Fv.Fm,col=treatment))+
  geom_point(shape=1,size=1)+
  geom_smooth(method=lm)+
  scale_color_brewer(palette = "Set1")+
  facet_wrap(.~Variety)`

That works very well, but I would like to annotate the r squared values for the regression lines. I have two treatments and 42 varieties, therefore 84 regression lines. Are there any possibilties to calculate all r squared values and integrate them into the ggplot? I found allready the function

ggplotRegression <- function (fit) {

require(ggplot2)

ggplot(fit$model, aes_string(x = names(fit$model)[2], y = names(fit$model)[1])) + 
geom_point() +
stat_smooth(method = "lm") +
labs(title = paste("Adj R2 = ",signif(summary(fit)$adj.r.squared, 5),
                   "Intercept =",signif(fit$coef[[1]],5 ),
                   " Slope =",signif(fit$coef[[2]], 5),
                   " P =",signif(summary(fit)$coef[2,4], 5)))
}

but that works just for one variety and one treatment. Could be a loop for the lm() function an option?

Answer 1

You can't apply different labels to different facet, unless you add another r^2 column to your data.. One way is to use geom_text, but you need to calculate the stats you need first. Below I show an example with iris, and for your case, just change Species for Variety, and so on

library(tidyverse)
# simulate data for 2 treatments
# d2 is just shifted up from d1
d1 <- data.frame(iris,Treatment="A")
d2 <- data.frame(iris,Treatment="B") %>% 
mutate(Sepal.Length=Sepal.Length+rnorm(nrow(iris),1,0.5))
# combine datasets
DF <- rbind(d1,d2) %>% rename(Variety = Species)

# plot like you did
# note I use "free" scales, if scales very different between Species
# your facet plots will be squished
g <- ggplot(DF,aes(x=Sepal.Width,y=Sepal.Length,col=Treatment))+
  geom_point(shape=1,size=1)+
  geom_smooth(method=lm)+
  scale_color_brewer(palette = "Set1")+
  facet_wrap(.~Variety,scales="free")

# rsq function
RSQ = function(y,x){signif(summary(lm(y ~ x))$adj.r.squared, 3)}
#calculate rsq for variety + treatment
STATS <- DF %>%
group_by(Variety,Treatment) %>% 
summarise(Rsq=RSQ(Sepal.Length,Sepal.Width)) %>%
# make a label
# one other option is to use stringr::str_wrap in geom_text
mutate(Label=paste("Treat",Treatment,", Rsq=",Rsq))

# set vertical position of rsq
VJUST = ifelse(STATS$Treatment=="A",1.5,3)
# finally the plot function
g + geom_text(data=STATS,aes(x=-Inf,y=+Inf,label=Label),
hjust = -0.1, vjust = VJUST,size=3)

For the last geom_text() call, I allowed the y coordinates of the text to be different by multiplying the Treatment.. You might need to adjust that depending on your plot..

Answer 2

Here is an example with the ggpmisc package:

library(ggpmisc)

set.seed(4321)
x <- 1:100
y <- (x + x^2 + x^3) + rnorm(length(x), mean = 0, sd = mean(x^3) / 4)
my.data <- data.frame(x = x, 
                      y = y,
                      group = c("A", "B"))
formula <- y ~ poly(x, 1, raw = TRUE)    
ggplot(my.data, aes(x, y)) + 
  facet_wrap(~ group) + 
  geom_point() +
  geom_smooth(method = "lm", formula = formula) +
  stat_poly_eq(formula = formula, parse = TRUE, 
               mapping = aes(label = stat(rr.label)))