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Map Functions Over Glycan Structure Vectors

smap.Rd

These functions apply a function to each unique structure in a glycan structure vector, taking advantage of hash-based deduplication to avoid redundant computation. Similar to purrr mapping functions, but optimized for glycan structure vectors.

Usage

smap(.x, .f, ..., .parallel = FALSE)

smap_vec(.x, .f, ..., .ptype = NULL, .parallel = FALSE)

smap_lgl(.x, .f, ..., .parallel = FALSE)

smap_int(.x, .f, ..., .parallel = FALSE)

smap_dbl(.x, .f, ..., .parallel = FALSE)

smap_chr(.x, .f, ..., .parallel = FALSE)

smap_structure(.x, .f, ..., .parallel = FALSE)

Arguments

.x

A glycan structure vector (glyrepr_structure).

.f

A function that takes an igraph object and returns a result. Can be a function, purrr-style lambda (~ .x$attr), or a character string naming a function.

...

Additional arguments passed to .f.

.parallel

Logical; whether to use parallel processing. If FALSE (default), parallel processing is disabled. Set to TRUE to enable parallel processing.

.ptype

A prototype for the return type (for smap_vec).

Value

  • smap(): A list

  • smap_vec(): An atomic vector of type specified by .ptype

  • smap_lgl/int/dbl/chr(): Atomic vectors of the corresponding type

  • smap_structure(): A new glyrepr_structure object

Details

These functions only compute .f once for each unique structure, then map the results back to the original vector positions. This is much more efficient than applying .f to each element individually when there are duplicate structures.

Return Types:

  • smap(): Returns a list with the same length as .x

  • smap_vec(): Returns an atomic vector with the same length as .x

  • smap_lgl(): Returns a logical vector

  • smap_int(): Returns an integer vector

  • smap_dbl(): Returns a double vector

  • smap_chr(): Returns a character vector

  • smap_structure(): Returns a new glycan structure vector (.f must return igraph objects)

Examples

# Create a structure vector with duplicates
core1 <- o_glycan_core_1()
core2 <- n_glycan_core()
structures <- glycan_structure(core1, core2, core1)  # core1 appears twice

# Map a function that counts vertices - only computed twice, not three times
smap_int(structures, igraph::vcount)
#> [1] 2 5 2

# Map a function that returns logical
smap_lgl(structures, function(g) igraph::vcount(g) > 5)
#> [1] FALSE FALSE FALSE

# Use purrr-style lambda functions  
smap_int(structures, ~ igraph::vcount(.x))
#> [1] 2 5 2
smap_lgl(structures, ~ igraph::vcount(.x) > 5)
#> [1] FALSE FALSE FALSE

# Map a function that modifies structure (must return igraph)
add_vertex_names <- function(g) {
  if (!("name" %in% igraph::vertex_attr_names(g))) {
    igraph::set_vertex_attr(g, "name", value = paste0("v", seq_len(igraph::vcount(g))))
  } else {
    g
  }
}
smap_structure(structures, add_vertex_names)
#> <glycan_structure[3]>
#> [1] Gal(b1-3)GalNAc(a1-
#> [2] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [3] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 2