Pass arguments into function within a function

Question

I am writing function that involve other function from base R with a lot of arguments. For example (real function is much longer):

myfunction <- function (dataframe, Colv = NA) { 
matrix <- as.matrix (dataframe) 
out <- heatmap(matrix, Colv = Colv)
return(out)
}

data(mtcars)

myfunction (mtcars, Colv = NA)

The heatmap has many arguments that can be passed to:

heatmap(x, Rowv=NULL, Colv=if(symm)"Rowv" else NULL,
        distfun = dist, hclustfun = hclust,
        reorderfun = function(d,w) reorder(d,w),
        add.expr, symm = FALSE, revC = identical(Colv, "Rowv"),
        scale=c("row", "column", "none"), na.rm = TRUE,
        margins = c(5, 5), ColSideColors, RowSideColors,
        cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc),
        labRow = NULL, labCol = NULL, main = NULL,
        xlab = NULL, ylab = NULL,
        keep.dendro = FALSE, verbose = getOption("verbose"), ...)

I want to use these arguments without listing them inside myfunction.

myfunction (mtcars, Colv = NA, col = topo.colors(16))
Error in myfunction(mtcars, Colv = NA, col = topo.colors(16)) : 
  unused argument(s) (col = topo.colors(16))

I tried the following but do not work:

myfunction <- function (dataframe, Colv = NA) { 
matrix <- as.matrix (dataframe) 
out <- heatmap(matrix, Colv = Colv, ....)
return(out)
}
data(mtcars)

myfunction (mtcars, Colv = NA, col = topo.colors(16))

joran · Accepted Answer · 2012-06-17 15:37:17Z

46

Try three dots instead of four, and add the ellipsis argument to the top level function:

myfunction <- function (dataframe, Colv = NA, ...) { 
    matrix <- as.matrix (dataframe) 
    out <- heatmap(matrix, Colv = Colv, ...)
    return(out)
}

answered Jun 17, 2012 at 15:37

joran

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5 Comments

Carl Witthoft Over a year ago

Just to add an option (or add confusion), you can augment the contents of ... by setting a variable inside your main function dotfuns<-list(..., other_variable) and passing that to subsequent functions. Do this at your own risk :-)

jon Over a year ago

@CarlWitthoft sorry I could not get what you mean, could exand your solution (perhaps as answer )

Carl Witthoft Over a year ago

It wasn't an answer to your specific problem, just a comment on other things that can be done with the ... collection of arguments.

Dimitrios Zacharatos Over a year ago

this answer is very helpful, I wonder if there is a solution when you have 2 different functions with different names of arguments

Alf Pascu Over a year ago

@DimitriosZacharatos when you have 2 or more different functions within your function you can specify lists of arguments, have a look at G. Grothendieck answer to this question.

Dragos Bandur · Accepted Answer · 2022-02-16 19:22:40Z

0

Try this:

arguments for heatmap in globalenv:

argsHeat = alist( <arguments for heatmap>)

Instead of calling heatmap() inside myfunction, do this

out = do.call('heatmap', args = argsHeat)

answered Feb 16, 2022 at 19:22

Dragos Bandur

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