无法正确返回for循环中的对象名称

Question

I'm trying to automate making a series of the same plot using different objects; I'm working with S4 class phyloseq objects. When I use a for loop to iterate over a list of objects and try to use the object name as a title for each plot and in a filename for ggsave I can't quite get it to recognize the correct name, though it's making the correct plots for a given object in the list.

I've tried using variations of deparse(substitute(object)) with get() and quote() and end up getting slightly different, but still off-target results.

    object_list <- c(object1, object2, object3)
    automate_graphs <- function(x){
      for(object in x){
        name <- deparse(substitute(object))
        ordination <- ordinate(object, "NMDS", "bray")
        plot <- plot_ordination(object, ordination) + ggtitle(label = name)
        ggsave(plot, filename=sprintf("NMDS_bray_%s.pdf", name), height=4, width=7)}}

    automate_graphs(object_list)

I'm expecting to save 3 pdfs named NMDS_bray_object1 , NMDS_bray_object2 , NMDS_bray_object3 .

Instead I get NMDS_bray_S4 object of class structure("phyloseq", package = "phyloseq") (so it's saving the deparse of the object to the variable name rather than the substitution) or with quote I get NMDS_bray_object which I suppose is to be expected haha. Thanks in advance for any help!

Answer 1

Just make it a named vector (list) of objects and iterate over the names:

object_list <- c(object1 = object1,object2 = object2,object3 = object3)

automate_graphs <- function(x){
    for(nm in names(x)){
        object <- x[nm] #Pick out the one named nm
        ordination <- ordinate(object, "NMDS", "bray")
        plot <- plot_ordination(object, ordination) + ggtitle(label = nm)
        ggsave(plot, filename=sprintf("NMDS_bray_%s.pdf", nm), height=4, width=7)
    }}

automate_graphs(object_list)

Answer 2

@Joran thanks again for the help--it pushed me in the right direction to figuring out a solution, even if it's not the most elegant. I took the idea of generating a vector of names and then just created an extra variable to cycle through that vector. But this way it maintains the class of object and creates a separate list of corresponding names:

object_list <- c("object1" = object1, "object2" = object2, "object3" = object3)
automate_graphs <- function(x){
  names = names(x)
  obj_num = 1
  for(object in x){
    name <- names[obj_num]
    ordination <- ordinate(object, "NMDS", "bray")
    plot <- plot_ordination(object, ordination) + ggtitle(label = name)
    ggsave(plot, filename=sprintf("NMDS_bray_%s.pdf", name), height=4, width=7)

    obj_num = obj_num + 1
  }
}
automate_graphs(object_list)