Position stacked identity data sample size as geom_text directly over a bar using geom

In this experiment, we tracked presence or absence of bacterial infection in our subject animals. We were able to isolate which type of bacteria was present in our animals and created a plot that has Week Since Experiment Start on the X axis, and Percentage of Animals Positive for bacterial infection on the Y axis. This is a stacked identity ggplot where each geom_bar contains the different identities of the bacteria that were in the infected animals each week. Here is a sample dataset with the corresponding ggplot code and result:

DummyData <- data.frame(matrix(ncol = 5, nrow = 78))

colnames(DummyData) <- c('WeeksSinceStart','BacteriaType','PositiveOccurences','SampleSize','NewSampleSize')

DummyData$WeeksSinceStart <- c(1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,8,8,8,8,8,8,8,9,9,9,9,9,10,10,10,10)

DummyData$BacteriaType <- c("BactA","BactB","BactD","BactB","BactE","BactA","BactS","BactF","BactE","BactH","BactJ","BactK","BactE","BactB","BactS","BactF","BactL","BactE","BactW","BactH","BactS","BactJ","BactQ","BactN","BactW","BactA","BactD","BactE","BactA","BactC","BactD","BactK","BactL","BactE","BactD","BactA","BactS","BactK","BactB","BactE","BactF","BactH","BactN","BactE","BactL","BactZ","BactE","BactC","BactR","BactD","BactJ","BactN","BactK","BactW","BactR","BactE","BactW","BactA","BactM","BactG","BactO","BactI","BactE","BactD","BactM","BactH","BactC","BactM","BactW","BactA","BactL","BactB","BactE","BactA","BactS","BactH","BactQ","BactF")

PosOcc <- seq(from = 1, to = 2, by = 1)
DummyData$PositiveOccurences <- rep(PosOcc, times = 13)

DummyData$SampleSize <- c(78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,78,29,29,29,29,29,10,10,10,10)


DummyData$NewSampleSize <- c(78,NA,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,NA,NA,78,NA,NA,NA,NA,NA,NA,29,NA,NA,NA,NA,10,NA,NA,NA)


numcolor <- 20
plotcolors <- colorRampPalette(brewer.pal(8, "Set3"))(numcolor)

#GGplot for Dummy Data
DummyDataPlot <- ggplot(DummyData, aes(x = WeeksSinceStart, y = PositiveOccurences/SampleSize, fill = BacteriaType))   geom_bar(position = "stack", stat = "identity")  
geom_text(label = DummyData$NewSampleSize, nudge_y = 0.1)  
  
scale_y_continuous(limits = c(0,0.6), breaks = seq(0, 1, by = 0.1))   scale_x_continuous(limits = c(0.5,11), breaks = seq(0,10, by =1))    
  labs(
  x = "Weeks Since Start",
  y = "Proportion Positive")  
scale_fill_manual(values = plotcolors)

The problem: I cannot seem to find a way to position the labels from geom_text directly over each bar. I would also love to add the text "n = " to the sample size value directly over each bar. Thank you for your help!

I have tried different values for position_dodge statement and nudge_y statement with no success.

CodePudding user response：

Sometimes the easiest approach is to do some data wrangling, i.e. one option would be to create a separate dataframe for your labels:

library(ggplot2)
library(dplyr)

dat_label <- DummyData |> 
  group_by(WeeksSinceStart) |> 
  summarise(y = sum(PositiveOccurences / SampleSize), SampleSize = unique(SampleSize))

ggplot(DummyData, aes(x = WeeksSinceStart, y = PositiveOccurences / SampleSize, fill = BacteriaType))  
  geom_bar(position = "stack", stat = "identity")  
  geom_text(data = dat_label, aes(x = WeeksSinceStart, y = y, label = SampleSize), inherit.aes = FALSE, nudge_y = .01)  
  #scale_y_continuous(limits = c(0, 0.6), breaks = seq(0, 1, by = 0.1))  
  scale_x_continuous(limits = c(0.5, 11), breaks = seq(0, 10, by = 1))  
  labs(
    x = "Weeks Since Start",
    y = "Proportion Positive"
  )  
  scale_fill_manual(values = plotcolors)