Partially change default values of arguments

This is the problem I have. For example, in the Heatmap() function in the ComplexHeatmap package, one of its argument row_title_gp has a default value gpar(fontsize = 13.2):

Heatmap = function(..., row_title_gp = gpar(fontsize = 13.2), ...) {
...
}

Here row_title_gp controls the graphics parameters for the row title and it accepts a list of other parameters, such as col and fontfamily. Now the problem is when users set row_title_gp with other parameters, e.g. to set the color of text, they must also set fontsize with its default value, even though when they only want to set the color. If they do not set fontsize, it will not use the default value of 13.2, while it will use the “global default” which is 12 (try get.gpar("fontsize")).

Heatmap(..., row_title_gp = gpar(fontsize = 13.2,  col = "red"))

This is tedious and user-unfriendly.

The good thing is, in the function arguments, explictely coding as row_title_gp = gpar(fontsize = 13.2) helps users to know that a specific default is set to the argument row_title_gp which is not the system-default one. But the bad thing is, users might forget to set fontsize at the same time if they set other parameters.

Now the question is: can the default paramters which are not modified by users be automatically saved? In the prevous example, when we set Heatmap(..., row_title_gp = gpar(col = "red")), can row_title_gp still use fontsize = 13.2?

One widely-used solution is to write a “control” function which controls the default parameters. For example, in the Mclust() function from the mclust package:

Mclust = function (..., control = emControl(), ...) {
...
}

There is a emControl() function which takes care of the default values.

library(mclust)
emControl()
## $eps ## [1] 2.220446e-16 ## ##$tol
## [1] 1.000000e-05 1.490116e-08
##
## $itmax ## [1] 2147483647 2147483647 ## ##$equalPro
## [1] FALSE

And if only change one parameter, default values for other parameters are still used:

emControl(eps = 1e-10)
## $eps ## [1] 1e-10 ## ##$tol
## [1] 1.000000e-05 1.490116e-08
##
## $itmax ## [1] 2147483647 2147483647 ## ##$equalPro
## [1] FALSE

Similarly, in ComplexHeatmap, to control the graphics parameters for axes, there is also a “control-like” function default_axis_param() which takes care of the default graphics parameters for axes.

Writing a “control” or “default_param” function is very helpful when the default parameter list is long. The drawback is also obvous. Users neeed to execute the “control” functions or go to the documentations to see the exact default values.

Now my question is, if the default parameters are still hard coded in the argument of the function, can we still keep the default parameters if they are not specified by users?

The solution is not difficult. If default parameters are coded in the argument, just extract them. Let’s take the argument row_title_gp in Heatmap() as an example.

Step 1: Get the new value of row_title_gp which is specified by users.

Heatmap = function(..., row_title_gp = gpar(fontsize = 13.2), ...) {
new = row_title_gp
...
}

Step 2: Get the default value of row_title_gp which is coded in the function definition.

This is a little bit tricky. If users have specified row_title_gp, its the default value is overwritten and not seeable in Heatmap(). Nevertheless, we can use sys.function() to get the function that was called by users (which is Heatmap()), next with the formals functions to obtain the argument lists, and finally evaluate the argument (with eval()) to obtain the default value of row_title_gp.

Heatmap = function(..., row_title_gp = gpar(fontsize = 13.2), ...) {
new = row_title_gp
fml = formals(sys.function(sys.parent(1)))
default = eval(fml[["row_title_gp"]])
...
}

Step 3: Merge the new value and default value.

The new code is very straightforward.

Heatmap = function(..., row_title_gp = gpar(fontsize = 13.2), ...) {
new = row_title_gp
fml = formals(sys.function(sys.parent(1)))
default = eval(fml[["row_title_gp"]])

dnm = setdiff(names(default), names(new))
if(length(dnm) > 0) {
for(n in dnm) lt[[n]] = default[[n]]
}
row_title_gp = new
...
}

Next we want to make this functionality more general. The following utility function mark_default() can be used inside any function which “marks” arguments to automatically reuse the default parameters.

mark_default = function(arg) {
e = parent.frame()
new = get(arg, envir = e)
fml = formals(sys.function(sys.parent(1)))
default = eval(fml[[arg]])

lt = new
dnm = setdiff(names(default), names(new))
if(length(dnm) > 0) {
for(n in dnm) lt[[n]] = default[[n]]
}

assign(arg, lt, envir = e)
invisible(lt)
}

Let me show you some simple experiments of mark_default().

In the first experiment, there are two default parameters for gp which are col and lty. As you can see, if only col is set, lty is lost.

library(grid)
draw_sth = function(gp = gpar(col = "red", lty = 2)) {
print(gp)
}
draw_sth(gp = gpar(col = "black"))
## $col ## [1] "black" Next, we simply add mark_default() inside draw_sth() and mark the argument gp. Now the default gpar(col = "red", lty = 2) can be reused. draw_sth = function(gp = gpar(col = "red", lty = 2)) { mark_default("gp") print(gp) } draw_sth(gp = gpar(col = "black")) ##$col
## [1] "black"
##
## $lty ## [1] 2 draw_sth(gp = gpar(lwd = 3)) ##$lwd
## [1] 3
##
## $col ## [1] "red" ## ##$lty
## [1] 2