Rarefaction curves in ggplot

Mon, Dec 17, 2018 9:57 AM

Hi Ellen,

I was curious about this because I will be using a lot of vegan functions in a spring class. Turns out not to be trivial - as with all ggplot problems the trick is to get the data into a dataframe. I tried several things, but ended up writing my own function:

# rarefraction curves and ggplot
library("tidyverse")
library("vegan")
data(BCI)
out <- rarecurve(BCI, step = 10, sample = 400)
names(out) <- 1:50

as_tibble_rc <- function(x){
  # convert rarecurve() output to data.frame
  # bind_rows doesn't work because items are different lengths
  # also need to extract sample sizes from attribute 
  # Allocate result dataframe
  nsamples <- map_int(x, length)
  total_samples <- sum(nsamples)
  if(!is.null(names(x))){
    sites <- names(x)
  } else {
    sites <- as.character(1:length(nsamples))
  }
  result <- data_frame(Site = rep("", total_samples),
                       Sample_size = rep(0, total_samples),
                       Species = rep(0, total_samples))
  start <- 1
  for (i in 1:length(nsamples)){
    result[start:(start + nsamples[i]-1), "Site"] <- sites[i]
    result[start:(start + nsamples[i]-1), "Sample_size"] <- attr(x[[i]], "Subsample")
    result[start:(start + nsamples[i]-1), "Species"] <- x[[i]]
    start <- start + nsamples[i]
  }
  result
}

out <- as_tibble_rc(out)
# add grouping variable
sitedata <- data_frame(Site = as.character(1:50),
                       Type = sample(LETTERS[1:2], 50, replace = TRUE))
alldata <- left_join(out, sitedata, by = "Site")

# and then it's trivial
ggplot(data = alldata,
       mapping = aes(x = Sample_size, y = Species, color = Type, group = Site)) + 
  geom_line()

hope that helps.

Drew Tyre
 
School of Natural Resources
University of Nebraska-Lincoln
416 Hardin Hall, East Campus
3310 Holdrege Street
Lincoln, NE 68583-0974
 
phone: +1 402 472 4054
fax: +1 402 472 2946
email: atyre2 at unl.edu
http://snr.unl.edu/tyre
http://drewtyre.rbind.io
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Excerpted from: Awakening Loving-Kindness by Pema Ch?dr?n
 

?On 12/17/18, 10:14 AM, "R-sig-ecology on behalf of Ellen Pape" <r-sig-ecology-bounces at r-project.org on behalf of ellen.pape at gmail.com> wrote:

    Hi all,
    
    As I use ggplot2 for all my graphs, I would like to use ggplot2 to
    construct rarefaction curves as well (I also want to combine 2 rarefaction
    curves in 1 plot using cowplot which also vows for using ggplot2).
    
    I made these rarefaction curves using the rarecurve function in vegan, but
    I don't see how I can use these results and put these in ggplot2.
    
    I found the following website during my search:
    https://urldefense.proofpoint.com/v2/url?u=https-3A__www.fromthebottomoftheheap.net_2015_04_16_drawing-2Drarefaction-2Dcurves-2Dwith-2Dcustom-2Dcolours_&d=DwICAg&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=aLEaSryyUcERVqcKVZl7lQ&m=ScKzUcnIZJ2da4_YAAzmizwFy-CbI90_F4SV_FKSLLc&s=-DiwE4s5JljqtJk5ZhKOE4Benr3yDXmDM19K7wNG3bI&e=
    but it does not explain how to draw rarefaction curves with ggplot2.
    
    This website mentions - and this is what I would like to be able to do in
    ggplot2:
    
    "Where I do think this sort of approach might work is if the samples in the
    data set come from a few different groups and we want to colour the curves
    by group.
    
    col <- c("darkred", "forestgreen", "hotpink", "blue")set.seed(3)grp <-
    factor(sample(seq_along(col), nrow(BCI2), replace = TRUE))cols <-
    col[grp]
    
    The code above creates a grouping factor grp for illustration purposes; in
    real analyses you'd have this already as a factor variable in you data
    somewhere. We also have to expand the col vector because we are plotting
    each line in a loop. The plot code, reusing elements from the previous
    plot, is shown below:
    
    plot(c(1, max(Nmax)), c(1, max(Smax)), xlab = "Sample Size",
         ylab = "Species", type = "n")abline(v = raremax)for (i in seq_along(out)) {
        N <- attr(out[[i]], "Subsample")
        lines(N, out[[i]], col = cols[i])}
    
    [image: An attempt at rarefaction curves output with custom colours per
    groups of curves.]An attempt at rarefaction curves output with custom
    colours per groups of curves.
    
    
    but I don't see how I adjust this code to make the same plot in ggplot2.
    
    
    
    Anyone?
    
    Thanks!
    Ellen
    
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Rarefaction curves in ggplot

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