r - Multiple side-by-side barplots grouped by one numerical variable

Question

I apologise for asking a simple question but I have tried to find a solution over the last couple of days. There are 8 levels under Sampling.Station.Number in the data frame below. Therefore, I am attempting to produce a side-by-side barplot showing three bars per sampling station for three bat species detected called: (1) Pipestrellus pygmaeus; (2) Pipestrellus pipestrellus; and (3)nyctalus noctula.

Any suggestions how to do that? I made some searches but I only find examples for factors on the x axis, not variables grouped by a numerical variable, any help will be appreciated!

In the end I want to produce a barplot that has the same format as this boxplot, which I constructed:

I created these boxplot's with this code below:

         Sampling.Station.labels=c("1","2","3","4","5","6","7","8")

         bat.labels<-c("Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula",
                       "Pipistrellus pygmaeus", "Pipestrellus pipestrellus", "Nyctalus noctula")


         data_long <- gather(bats1, x, Mean.Value, Saparano.Pipestrelle:Noctule)
         head(data_long) 

         stacked.data.1<-melt(data_long, id=c('Sampling.Station', 'x'))
         head(stacked.data.1)
         str(stacked.data.1)


         stacked.data.1=stacked.data.1[, -3]
         head(stacked.data.1)
         colnames(stacked.data.1)<-c("Sampling.Station", "Bat.Species", "Light.Intensity") 
         head(stacked.data.1)


         par(mfrow = c(1,1))
         boxplots.double.1=boxplot(Lighty.Intensity~Sampling.Station + Bat.Species, 
                                   data = stacked.data.1, 
                                   at = c(1:24), 
                                   ylim = c(min(0, min(0)), 
                                            max(30, na.rm = T)),
                                   xaxt = "n",
                                   notch=TRUE,
                                   col = c("red", "blue", "green"),
                                   cex.axis=0.7,
                                   cex.labels=0.7,
                                   ylab="Light Intensity (Lux)", 
                                   xlab="Sampling Stations",
                                   space=1)

         axis(side = 1, at = seq(3, 24, by = 1), labels = FALSE)
         text(seq(3, 24, by=3), par("usr")[3] - 0.2, labels=unique(Sampling.Station.labels), srt = 45, pos = 1, xpd = TRUE, cex=0.8)
         par(oma = c(4, 1, 1, 1))
         par(fig = c(0, 1, 0, 1), oma = c(0, 0, 0, 0), mar = c(0, 0, 0, 0), new = TRUE)
         plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
         legend("top", 
                legend=c("Pipistrellus pygmaeus","Pipestrellus pipestrellus","Nyctalus noctula"),
                fill=c("Blue", "Red", "Green"),
                xpd = TRUE, horiz = TRUE, 
                inset = c(0,0), 
                bty = "n", 
                col = 1:4, 
                cex = 0.8,
                title = "Bat Species",
                lty = c(1,1))

I tried Richard's suggestion but I am still experiencing this error message, would anyone be able to help. Many thanks in advance if this is possible:

   data=format

   Data structure: 

   'data.frame':    144 obs. of  5 variables:
     $ Sampling.Station    : num  1 1 1 2 2 2 3 3 3 4 ...
     $ Light.Intensity.S   : num  26.9 25.2 39 29.8 21.8 ...
     $ Number.of.bat.passes: num  3 2 5 6 15 2 10 12 17 2 ...
     $ Bat.Species         : Factor w/ 3 levels       "Common.Pipestrelle",..: 3 3 3 3 3 3 3 3 3 3 ...
     $ Simpsons.Index      : num  0.4444 0 0 0.0278 0 ...

       df %>% 
       gather(key = bat.species, value = value, -station) %>%
       mutate(station = as.factor(station)) %>%
       ggplot(aes(x = station, y = value, colour = variable)) +
       geom_boxplot() + 
       facet_grid(~bat.species, scales = "free_y")


       **Error in eval(expr, envir, enclos) : object 'Sampling.Station' not found**

Dataframe

bats1<-structure(list(Sampling.Station = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 
4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 8, 2, 2, 2, 3, 3, 3, 
4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 8, 1, 1, 1, 1, 1, 1, 
2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 8, 
2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 8, 
1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6, 
7, 7, 7, 8, 8, 8, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6, 
7, 7, 7, 8, 8, 8, 1, 1, 1), Light.Intensity = c(26.9, 25.16, 
39, 29.81, 21.83, 20.22, 2.9, 2.1, 0.85, 0.62, 0.39, 0.26, 24.7, 
21.99, 20.46, 26.32, 0, 0, 0.43, 0.02, 0.02, 0.03, 0.02, 0.03, 
 293.56, 167.79, 114.06, 17.22, 16.26, 4.76, 0.63, 0.56, 0.56, 
 86.63, 87.97, 88.59, 0.31, 0.04, 0.05, 0, 0.01, 0.01, 0.02, 2.6, 
 2.68, 2.62, 0.43, 0.44, 26.9, 25.16, 39, 29.81, 21.83, 20.22, 
 2.9, 2.1, 0.85, 0.62, 0.39, 0.26, 24.7, 21.99, 20.46, 26.32, 
 0, 0, 0.43, 0.02, 0.02, 0.03, 0.02, 0.03, 293.56, 167.79, 114.06, 
 17.22, 16.26, 4.76, 0.63, 0.56, 0.56, 86.63, 87.97, 88.59, 0.31, 
 0.04, 0.05, 0, 0.01, 0.01, 0.02, 2.6, 2.68, 2.62, 0.43, 0.44, 
 26.9, 25.16, 39, 29.81, 21.83, 20.22, 2.9, 2.1, 0.85, 0.62, 0.39, 
  0.26, 24.7, 21.99, 20.46, 26.32, 0, 0, 0.43, 0.02, 0.02, 0.03, 
  0.02, 0.03, 293.56, 167.79, 114.06, 17.22, 16.26, 4.76, 0.63, 
  0.56, 0.56, 86.63, 87.97, 88.59, 0.31, 0.04, 0.05, 0, 0.01, 0.01, 
  0.02, 2.6, 2.68, 2.62, 0.43, 0.44), Number.of.bat.passes = c(3, 
  2, 5, 6, 15, 2, 10, 12, 17, 2, 0, 0, 15, 7, 17, 0, 1, 0, 14, 
  10, 12, 7, 4, 1, 3, 5, 3, 1, 6, 11, 3, 0, 0, 12, 11, 9, 1, 2, 
  1, 12, 14, 10, 3, 2, 1, 5, 4, 2, 3, 2, 5, 6, 15, 2, 10, 12, 17, 
  2, 0, 0, 15, 7, 17, 0, 1, 0, 14, 10, 12, 7, 4, 1, 3, 5, 3, 1, 
  6, 11, 3, 0, 0, 12, 11, 9, 1, 2, 1, 12, 14, 10, 3, 2, 1, 5, 4, 
  2, 3, 2, 5, 6, 15, 2, 10, 12, 17, 2, 0, 0, 15, 7, 17, 0, 1, 0, 
  14, 10, 12, 7, 4, 1, 3, 5, 3, 1, 6, 11, 3, 0, 0, 12, 11, 9, 1, 
  2, 1, 12, 14, 10, 3, 2, 1, 5, 4, 2), Bat.Species = structure(c(3L, 
  3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
  3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
  3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 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, 1L, 1L, 1L, 1L, 1L, 1L, 
  1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 
  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
  2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label =           c("Common.Pipestrelle", 
 "Noctule", "Saprano.Pipestrelle"), class = "factor"), Simpsons.Index =           c(0.444444444, 
  0, 0, 0.027777778, 0, 0, 0.25, 0, 0.08650519, 0, 0, 0, 0.111111111, 
  0, 0.124567474, 0, 0, 0, 0.25, 0.01, 0.111111111, 0.081632653, 
  0, 0, 0, 0.04, 0, 1, 0.027777778, 0.033057851, 0.111111111, 0, 
  0, 0.027777778, 0.074380165, 0.012345679, 0, 0, 1, 0.173611111, 
  0.081632653, 0.16, 1, 0.25, 0, 0.04, 0.25, 0.25, 0.25, 0, 0, 
  7, 0, 0, 0, 0, 0.08, 0, 0, 0, 0.6, 0, 0.222222222, 0, 0, 0, 0.142857143, 
  9, 0.5, 1.25, 0, 0, 0, 4, 0, 0, 5, 2, 1, 0, 0, 1.25, 0.888888889, 
  5, 0, 0, 2, 0.28, 0.625, 0.375, 0, 1, 0, 4, 0.5, 1, 0, 0, 1, 
  0, 0.109375, 0, 0, 0, 0.75, 0, 0, 0, 0, 0.08, 0.046875, 0, 0, 
  0, 0, 0, 0.046875, 0, 0, 0, 0, 0.0625, 0, 0, 0, 0.015625, 0, 
  0, 0, 0.28, 0, 0.12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names =    c(NA, 
  -144L), .Names = c("Sampling.Station", "Light.Intensity",         "Number.of.bat.passes", 
   "Bat.Species", "Simpsons.Index"), class = "data.frame")

Answer 1

I am not exactly sure what you are after. This is what I would do with these data. I've used boxplots rather than barcharts as I think the latter are generally fairly useless for displaying variation.

library("dplyr")
library("tidyr")
library("ggplot2")

df %>% 
  gather(key = variable, value = value, -Sampling.Station.Number) %>%
  mutate(Sampling.Station.Number = as.factor(Sampling.Station.Number)) %>%
  ggplot(aes(x = Sampling.Station.Number, y = value, colour = variable)) +
  geom_boxplot() + 
  facet_wrap(~variable, scales = "free_y")

Data

df <- structure(list(Sampling.Station.Number = c(1L, 1L, 1L, 2L, 2L, 
2L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 
8L, 8L, 8L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 
6L, 6L, 7L, 7L, 7L, 8L, 8L, 8L, 1L, 1L, 1L), Spectrometer = c(26.9, 
25.16, 39, 29.81, 21.83, 20.22, 2.9, 2.1, 0.85, 0.62, 0.39, 0.26, 
24.7, 21.99, 20.46, 26.32, 0, 0, 0.43, 0.02, 0.02, 0.03, 0.02, 
0.03, 293.56, 167.79, 114.06, 17.22, 16.26, 4.76, 0.63, 0.56, 
0.56, 86.63, 87.97, 88.59, 0.31, 0.04, 0.05, 0, 0.01, 0.01, 0.02, 
2.6, 2.68, 2.62, 0.43, 0.44), D.SP = c(0.667, 0, 0, 0.167, 0, 
0, 0.5, 0, 0.294, 0, 0, 0, 0.333, 0, 0.353, 0, 0, 0, 0.5, 0.1, 
0.333, 0.286, 0, 0, 0, 0.2, 0, 1, 0.167, 0.182, 0.333, 0, 0, 
0.167, 0.273, 0.111, 0, 0, 1, 0.417, 0.286, 0.4, 1, 0.5, 0, 0.2, 
0.5, 0.5), D.CP = c(0.333, 1, 0.4, 1.167, 0.533, 1, 0, 0.167, 
0.118, 0, 0, 0, 1, 0.714, 0.471, 0, 1, 0, 0.5, 0.9, 0.667, 0.714, 
1, 1, 1, 0.8, 1, 0, 0.833, 0.727, 0.333, 0, 0, 0.417, 0.727, 
0.556, 1, 1, 2, 0.583, 0.714, 0.6, 0, 0.5, 1, 0.8, 0.5, 0.5), 
    D.N = c(0, 0, 0.8, 0, 0.467, 0, 0, 0, 0.176, 1, 0, 0, 0, 
    0.286, 0.176, 0, 0, 0, 0, 0, 0.25, 0, 0, 0, 0, 0.2, 0, 0, 
    0, 0.091, 0, 0, 0, 0.583, 0, 0.333, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0)), .Names = c("Sampling.Station.Number", "Spectrometer", 
"D.SP", "D.CP", "D.N"), class = "data.frame", row.names = c("1", 
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", 
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", 
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", 
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", 
"47", "48"))