provide sample size for violin plot - r

Question

Using the following code I made a violin plot for most of my variables, and added points where I didn't have sufficient information for some data. I'd like to add sample sizes to the right end of each violin, but I haven't been able to find a way to do this.
#dataset
str(threats)
'data.frame': 60 obs. of 3 variables:
$ threat : Factor w/ 7 levels "weather","competition",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Species : Factor w/ 5 levels "Bank","Barn",..: 1 1 1 1 1 1 1 1 1 1 ...
$ effect.abs : int 18 13 0 43 43 0 23 13 14 16 ...
#added to help 0 values with logarithmic axis scale
threats$effect.abs1<-threats$effect.abs+0.1
#subset of data with insufficient info for violin plot
#plotted with geom_dotplot
threats.sub<-subset(threats,
(threat=="competition") |
(threat=="disease" & Species =="Barn") |
(threat=="insect_availability") |
(threat=="weather" &
(Species=="Cliff" | Species=="Purple")) |
(threat=="incidental_loss") |
(threat=="predation" & Species=="Bank"))
ggplot() +
geom_dotplot(data=threats.sub, aes(x=Species, y=effect.abs1, fill=Species),
binaxis='y', stackdir='center', binwidth =.1) +
geom_violin(data=threats, aes(x=Species, y=effect.abs1, fill=Species)) +
coord_flip() +
facet_wrap(~threat, ncol=2, labeller = labeller(threat=facet.labels),
strip.position = "left") +
scale_y_log10(breaks=c(0.1,1,10,100), labels=c(0,1,10,100)) +
labs(x=("Threat"), y=("Absolute effect on adult survival (%)")) +
theme_bw() +
theme(axis.text=element_text(size=9, colour="black"),
axis.title=element_text(size=10, colour="black"),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
panel.grid=element_blank(),
panel.border=element_rect(colour="black", size=1),
plot.margin=unit(c(.3,.3,.4,.4), "cm"),
strip.background=element_rect(fill=NA, colour=NA), #element_blank(),
legend.position="right")
My attempts to use the solution below (provided in other questions), only resulted in an error message.
give.n <- function(x){
return(c(y = mean(x), label = length(x)))
}
stat_summary(fun.data = give.n, geom = "text") #added to ggplot code above
Error in if (empty(data)) { : missing value where TRUE/FALSE needed
I would appreciate any help with this issue. I'd prefer to find a way for R to calculate the sample sizes (rather then me providing each one), as I also keep getting this following warning message when I produce this figure and I'd like to double-check that all the data is being displayed correctly.
Warning messages:
1: In max(data$density) : no non-missing arguments to max; returning -Inf
2: In max(data$density) : no non-missing arguments to max; returning -Inf
3: In max(data$density) : no non-missing arguments to max; returning -Inf
Thanks!
As requested:
structure(list(threat = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
7L, 7L, 7L, 7L, 7L), .Label = c("weather", "competition", "incidental_loss",
"contaminants", "insect_availability", "disease", "predation"
), class = "factor"),
Species = structure(c(1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 5L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L,
5L, 5L, 1L, 2L, 2L, 2L, 2L), .Label = c("Bank", "Barn", "Cliff",
"Tree", "Purple"), class = "factor"),
effect.abs = c(18L,
13L, 0L, 43L, 43L, 0L, 23L, 13L, 14L, 16L, 18L, 29L, 0L, 40L,
0L, 20L, 53L, 0L, 17L, 15L, 13L, 25L, 19L, 25L, 0L, 0L, 0L, 14L,
20L, 0L, 0L, 0L, 0L, 4L, 1L, 0L, 1L, 1L, 1L, 1L, 12L, 0L, 30L,
95L, 10L, 3L, 7L, 12L, 14L, 100L, 0L, 23L, 13L, 5L, 0L, 58L,
20L, 4L, 9L, 0L)), row.names = c(NA, -60L), class = "data.frame")

Answer 1

The way to tackle this is to precompute your n's
E.G.
summary_df <- df %>%
group_by(threat, Species, effect.abs1) %>%
summarise(n = n())
Then add it to your graph
+ geom_label(aes(x = 100, y = effect.abs1, label = n), data = summary_df)

Answer 2

Thanks for helpful comments from #Jack Brookes for getting me started on this. Here is my final solution for this issue.
#first summarize n's for all data
summary_df_all <- threats %>%
group_by(threat, Species) %>%
summarise(n = n(), maxE=max(effect.abs1))
#next summarize n's for the subset of data I'm not interested in getting the n's for
summary_df_sub <- threats.sub %>%
group_by(threat, Species) %>%
summarise(n = n(), maxE=max(effect.abs1)) %>%
mutate(probability = 0)
#combine these summaries, and filter out the points that will not be displayed
summary_df_violin <- left_join(summary_df_all, summary_df_sub,
by = c("threat", "Species")) %>%
mutate(probability = ifelse(is.na(probability), 1,
probability)) %>% filter(probability > 0)
#and plot
ggplot() +
geom_dotplot(data=threats.sub, aes(x=Species, y=effect.abs1, colour=Species, fill=Species),
binaxis='y', stackdir='center', binwidth =.09) +
geom_violin(data=threats, aes(x=Species, y=effect.abs1, colour=Species, fill=Species), size=1.1) +
#geom_label(aes(x=100, y=effect.abs1, label=n), data=summary_df)
geom_text(data=summary_df_violin, aes(y=maxE.x, x=Species, label=n.x), nudge_y=.2) +
coord_flip() +
facet_wrap(~threat, ncol=2, labeller = labeller(threat=facet.labels),
strip.position = "left") +
scale_y_log10(breaks=c(0.1,1,10,100), labels=c(0,1,10,100)) +
labs(x=("Threat"), y=("Absolute effect on adult survival (%)")) +
theme_bw() +
theme(axis.text=element_text(size=9, colour="black"),
axis.title=element_text(size=10, colour="black"),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
panel.grid=element_blank(),
panel.border=element_rect(colour="black", size=1),
plot.margin=unit(c(.3,.3,.4,.4), "cm"),
strip.background=element_rect(fill=NA, colour=NA),
strip.text=element_text(size=9, colour="black"),
legend.position="right")