Wsrtjtyk

I'm generating and plotting multiple ggplots based on data from two lists, therefore I'm using mapply. One of the lists has named elements, which I would like to use as ggtitle. But it only takes the first element for all the plots

> names(sample_subset_list)

[1] "water after day 43 dna min reads per OTU 5"

[2] "biofilm after day 43 dna min reads per OTU 5"

[3] "water after day 43 cdna min reads per OTU 5"

[4] "biofilm after day 43 cdna min reads per OTU 5"

[5] "water after day 44 dna min reads per OTU 5"

[6] "biofilm after day 44 dna min reads per OTU 5"

[7] "water after day 44 cdna min reads per OTU 5"

[8] "biofilm after day 44 cdna min reads per OTU 5"

and this is the plotting function:

ordination_plots <- list()

counter <- 0

ordination_plots <- mapply(function(x,y,counter) {

                        counter <- counter + 1 

                        plot_ordination(x, y, type = "sample") + 

                            ggtitle(names(sample_subset_list)[counter]) +

}, x = sample_subset_list, y = ordination_nmds, counter = 0, SIMPLIFY = FALSE)

this will give me plots where the title is always the first element of

names(sample_subset_list).

The same happens calling ggtitle(names(sample_subset_list)) +

If I use counter <<- (suggested here: Using a counter inside an apply structured loop in R) or call ggtitle like

ggtitle(names(sample_subset_list)) +

or

ggtitle(names(sample_subset_list)[]) +

I get no title at all.

I started without a counter, which also gave me the same title for all plots. Could someone explain to me how I can iterate over the names of the list elements to use them for the ggplots?

Let's reduce the complexity of the example:

counter <- 0



invisible(mapply(function(letter, counter) {



  counter <- counter + 1

  cat("Letter: ", letter, "; Counter: ", counter, "n", sep="")



}, letters[1:10], counter))

NOTE: I only used invisible() to stop printing the result of mapply().

letters[1:10] is a 10-element vector of lower-case letter (built in data).

You define counter outside of mapply(). Unlike for or while, functions in mapply() do not — by default — create or modify variables in the parent scope (outside of mapply(), so the result is this:

Letter: a; Counter: 1

Letter: b; Counter: 1

Letter: c; Counter: 1

Letter: d; Counter: 1

Letter: e; Counter: 1

Letter: f; Counter: 1

Letter: g; Counter: 1

Letter: h; Counter: 1

Letter: i; Counter: 1

Letter: j; Counter: 1

It's fine to pass in a second parameter with info to the function argument of mapply() but if the intent is to have a side-effect of incrementing something outside the scope of the function in mapply() then you really shouldn't pass it to in as parameter and just modify it using the <<- operator, which — according to the help page:

"The operators <<- and ->> are normally only used in functions, and cause a search to be made through parent environments for an existing definition of the variable being assigned. If such a variable is found (and its binding is not locked) then its value is redefined, otherwise assignment takes place in the global environment."

So, we can just do this:

# TO MY FUTURE SELF AND TEAM MEMBERS

# `counter` is modified as a side-effect of operations in the `mapply()`

# that follows the object declaration

counter <- 0



invisible(mapply(function(letter) {



  counter <<- counter + 1

  cat("Letter: ", letter, "; Counter: ", counter, "n", sep="")



}, letters[1:10]))

to get this:

Letter: a; Counter: 1

Letter: b; Counter: 2

Letter: c; Counter: 3

Letter: d; Counter: 4

Letter: e; Counter: 5

Letter: f; Counter: 6

Letter: g; Counter: 7

Letter: h; Counter: 8

Letter: i; Counter: 9

Letter: j; Counter: 10

The comment was not meant for snark. You are using a side-effect that may be non-obvious to your future self or folks you share the code with so noting it will help you re-figure out and them figure out what's happening.