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Here is what it looks like after those edits - lines but no boxes. new image

Reproducible code:

df <- data.frame(SampleID = structure(c(5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("C004", "C005", "C007", "C009", "C010", "C011", "C013", "C027", "C028", "C029", "C030", "C031", "C032", "C033", "C034", "C035", "C036", "C042", "C043", "C044", "C045", "C046", "C047", "C048", "C049", "C058", "C086"), class = "factor"), Sequencing.Depth = c(1L, 2612L, 5223L, 7834L, 10445L, 13056L, 15667L, 18278L, 20889L, 23500L), Observed.OTUs = c(1, 213, 289.5, 338, 377.8, 408.9, 434.4, 453.8, 472.1, NA), Mange = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("N", "Y"), class = "factor"), SpeciesCode = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("Cla", "Ucin", "Vvu"), class = "factor"))
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    I think it would be easier to help, if you provide a reproducible chunk of your data. So far, I can tell that it needs different data (like median or mean) with layers like geom_point or geom_path, compared to geom_boxplot. Commented Apr 14, 2020 at 20:20
  • Please take a look at How to make a great R reproducible example, to modify your question, with a smaller sample taken from your data (check ?dput()). Commented Apr 14, 2020 at 20:21
  • Does this answer your question? Joining means on a boxplot with a line (ggplot2) Commented Apr 14, 2020 at 20:37

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In your aes, you can use interaction of your x values and your categorical values for plotting boxplot on a continuous x axis and pass position = "identity" in order to place them on the precise x values and not to be dodged.

Here to add the line connecting each boxplot, I calculate mean per Species per x values using dplyr directly inggplot but you can calculate outside and generate a second dataframe.

So, as your x values are pretty spread from 1 to 23500, you will have to modify the width of the geom_boxplot in order to see a box and not a single line:

library(ggplot2) library(dplyr) ggplot(df,aes(x = Xvalues, y = Yvalues, color = Species, group = interaction(Species, Xvalues)))+ geom_boxplot(position = "identity", width = 1000)+ geom_line(data = df %>% group_by(Xvalues, Species) %>% summarise(Mean = mean(Yvalues)), aes(x = Xvalues, y = Mean, color = Species, group = Species))

enter image description here

So, apply to your dataset (based on informations you provided in your code), you should try something like: 

library(ggplot2) library(dplyr) ggplot(observedotusrare, aes(x=Sequencing.Depth, y=Observed.OTUs, color=SpeciesCode, group = interaction(Sequencing.Depth, SpeciesCode))) + geom_boxplot(position = "identity", width = 1000) + geom_line(data = observedotusrare %>% group_by(Sequencing.Depth, SpeciesCode) %>% summarise(Mean = mean(Observed.OTUs, na.rm = TRUE)), aes(x = Sequencing.Depth, y = Mean, color = SpeciesCode, group = SpeciesCode))

Does it answer your question ?

Reproducible example

df <- data.frame(Xvalues = rep(c(10,2000,23500), each = 30), Species = rep(rep(LETTERS[1:3], each = 10),3), Yvalues = c(rnorm(10,1,1), rnorm(10,5,1), rnorm(10,8,1), rnorm(10,5,1), rnorm(10,8,1), rnorm(10,12,1), rnorm(10,20,1), rnorm(10,30,1), rnorm(10,50,1)))
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3 Comments

almost worked. The lines appear now but the boxes for the boxplot still aren't there. Sorry I'm not super experienced with Stackoverflow, I'm not sure how to show a picture of what it looks like.
Ok, so we are on the right way. To add a picture, just edit your question and pictures as you didi in the first place. Also, please provide a reproducible example by adding the output of dput(head(observedotusrare,10)).
Thanks for providing additional info on your dataset. In fact, boxplots were traced on your graph but their width were so small compared to the range of x values that it looks like a single line. If you add width = 1000 into geom_boxplot you will be able to see them. Please check my edited answer and let me know if it is working for you.

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