Drawing rarefaction curves with custom colours
I was sent an email this week by a vegan user who wanted to draw rarefaction curves using
rarecurve() but with different colours for each curve. The solution to this one is quite easy as
rarecurve() has argument
col so the user could supply the appropriate vector of colours to use when plotting. However, they wanted to distinguish all 26 of their samples, which is certainly stretching the limits of perception if we only used colour. Instead we can vary other parameters of the plotted curves to help with identifying individual samples.
To illustrate, I’ll use the Barro Colorado Island data set
BIC that comes with vegan. I just take the first 26 samples as this was the data set size my correspondent indicated they had available.
raremax is the minimum sample count achieved over the 26 samples. We will rarefy the sample counts to this value.
To set up the parameters we might use for plotting,
expand.grid() is a useful helper function
Then we can call
rarecurve() as follows with the new graphical parameters
Note that I saved the output from
rarecurve() in object
out. This object contains everything we need to draw our own version of the plot if we wish. For example, we could use fewer colours and alter the line thickness1 instead to make up the required number of combinations.
Using the information in
out returned by
rarecurve() we can get almost the same plot using the following code to draw the elements by hand
Having done this, I don’t believe this is a useful graphic because we’re trying to distinguish between too many samples using graphical parameters. 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.
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:
We can’t use the approach outlined in this example to vary
lwdbecause of the way
rarecurve()draws the individual curves, in a loop. We have no way to tell
rarecurve()to use the ith element of a vector of
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By Gavin Simpson
16 April 2015