Hello,

I wrote a custom import function for the DataTrack constructor in Gviz (detailed here) to allow visualisation of stranded RNAseq data. In that example I hard coded the library orientation but would now like to provide an additional argument to the custom import function that specifies the library orientation.

However, I can't seem to pass additional arguments to the custom function e.g. these both fail (where strandedBamImport is the custom function and libType is the additional argument):

dataTrack = DataTrack(bamFile, genome="hg19", chromosome=myChr, importFunction=strandedBamImport, libType="fr-firststrand", stream=TRUE)

and

dataTrack = DataTrack(bamFile, genome="hg19", chromosome=myChr, importFunction=strandedBamImport(libType="fr-firststrand"), stream=TRUE)

Other than setting a global variable, is there a way around this that I am missing?

You cannot pass arguments to a function that are not already specified in the API. In other words, if you have a function

fun <- function(arg1, arg2)  cat(paste("I don't do anything, haha!\nBut here are your stupid args:\n", arg1, "\n", arg2, "\n"))

You cannot pass in arguments that don't exist:

> fun("this","that")
I don't do anything, haha!
But here are your stupid args:
 this
 that
> fun("this","that", nonexistentarg = "really?")
Error in fun("this", "that", nonexistentarg = "really?") :
  unused argument (nonexistentarg = "really?")

If you want to pass in arbitrary arguments you need the ellipsis (...) argument.

> fun <- function(arg1, arg2, ...)  cat(paste("I don't do anything, haha!\nBut here are your stupid args:\n", arg1, "\n", arg2, "\n"))
> fun("this","that", nonexistentarg = "really?")
I don't do anything, haha!
But here are your stupid args:
 this
 that

Which doesn't help with this stupid example, but say you have something else.

> fun <- function(vals, ...) plot(vals, ...)
> fun(1:10)
> fun(1:10, main = "Look Ma! Sweet R plot.")
> fun(1:10, main = "Whatevs", xlab = "something", ylab = "or other")

Now you can pass arbitrary commands to other functions, but only if a.) you use the ellipsis in your calls to sub-functions, and b.) the sub-functions have arguments with that name, and c.) you use argument names (e.g., you cannot use positional arguments for any arguments past the ellipsis). In other words,

> fun <- function(x, ..., y) plot(x,y, ...)
> fun(1:10, 2:11)
Error in plot(x, y, ...) (from #1) :
  error in evaluating the argument 'y' in selecting a method for function 'plot': Error: argument "y" is missing, with no default
> fun(1:10, y = 2:11, main = "MAIN TITLE")