# Efficient Glycan Manipulation with smap

## Overview

This vignette introduces the `smap` family of functions. These functions are useful when you want to apply custom `igraph`-based operations to glycan structure vectors.

This guide assumes you are comfortable with R programming and have some familiarity with graph concepts. If you are just getting started, read the “Getting Started with glyrepr” vignette first.

    library(glyrepr)

## Unique Structure Optimization

Before using `smap`, it helps to understand why these functions exist.

### The Problem

Working with glycan structures means working with graphs, and graph operations are computationally expensive. When you are analyzing thousands of glycans from a large-scale study, this becomes a real bottleneck.

### The Solution

`glyrepr` implements an optimization called unique structure storage. Instead of storing thousands of identical graphs, it stores only the unique ones and keeps track of which original positions they belong to.

Let’s see this in action:

    # Our test data: some common glycan structures
    iupacs <- c(
      "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-",  # N-glycan core
      "Gal(b1-3)GalNAc(a1-",                                    # O-glycan core 1
      "Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-",                     # O-glycan core 2
      "Man(a1-3)[Man(a1-6)]Man(a1-3)[Man(a1-6)]Man(a1-",          # Branched mannose
      "GlcNAc6Ac(b1-4)Glc3Me(a1-"                              # With decorations
    )

    struc <- as_glycan_structure(iupacs)

    # Now create a realistic dataset with lots of repetition.
    large_struc <- rep(struc, 1000)  # 5,000 total structures
    large_struc
    #> <glycan_structure[5000]>
    #> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
    #> [2] Gal(b1-3)GalNAc(a1-
    #> [3] Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
    #> [4] Man(a1-3)[Man(a1-6)]Man(a1-3)[Man(a1-6)]Man(a1-
    #> [5] GlcNAc6Ac(b1-4)Glc3Me(a1-
    #> [6] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
    #> [7] Gal(b1-3)GalNAc(a1-
    #> [8] Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
    #> [9] Man(a1-3)[Man(a1-6)]Man(a1-3)[Man(a1-6)]Man(a1-
    #> [10] GlcNAc6Ac(b1-4)Glc3Me(a1-
    #> ... (4990 more not shown)
    #> # Unique structures: 5

Notice that the object reports only 5 unique structures. The vector has 5,000 elements, but only 5 unique graphs are stored internally.

We can verify that directly:

    # Only 5 unique graphs are stored internally
    length(attr(large_struc, "structures"))
    #> [1] 0

    # But we have 5,000 total elements
    length(large_struc)
    #> [1] 5000

### Memory Savings

    library(lobstr)
    #> Warning: 程序包'lobstr'是用R版本4.5.2 来建造的
    obj_sizes(struc, large_struc)
    #> * 13.78 kB
    #> * 40.69 kB

The memory difference can be substantial. For repeated structures, the optimized representation can be much smaller than storing every graph independently.

## The `smap` Family

There is one important consequence of this internal representation: regular `lapply()` or `purrr::map()` functions do not operate directly on a glycan structure vector as if it were a list of graphs.

    # This will not work and will raise an error.
    tryCatch(
      purrr::map_int(large_struc, ~ igraph::vcount(.x)),
      error = function(e) cat("Error:", rlang::cnd_message(e))
    )
    #> Error: ℹ In index: 1.
    #> Caused by error in `ensure_igraph()`:
    #> ! Must provide a graph object (provided wrong object type).

Why does this fail? Because `purrr` functions don’t understand the internal structure optimization of `glycan_structure` objects.

### Structure-Aware Mapping

The `smap` functions are structure-aware alternatives to `purrr` mapping functions. They understand the unique structure optimization and work directly with the underlying graph objects.

    vertex_counts <- smap_int(large_struc, ~ igraph::vcount(.x))
    vertex_counts[1:10]
    #>  [1] 5 2 3 5 2 5 2 3 5 2

The “s” stands for “structure”: these functions operate on the underlying `igraph` objects that represent glycan structures.

## The `smap` Toolkit

The `smap` family provides glycan-aware equivalents for virtually all `purrr` functions:

purrr | smap | purrr | smap
--- | --- | --- | ---
`map()` | `smap()` | `map2()` | `smap2()`
`map_lgl()` | `smap_lgl()` | `map2_lgl()` | `smap2_lgl()`
`map_int()` | `smap_int()` | `map2_int()` | `smap2_int()`
`map_dbl()` | `smap_dbl()` | `map2_dbl()` | `smap2_dbl()`
`map_chr()` | `smap_chr()` | `map2_chr()` | `smap2_chr()`
`some()` | `ssome()` | `pmap()` | `spmap()`
`every()` | `severy()` | `pmap_*()` | `spmap_*()`
`none()` | `snone()` | `imap()` | `simap()`
|  | `imap_*()` | `simap_*()`

As a simple rule, replace `map` with `smap`, `pmap` with `spmap`, and `imap` with `simap`. The function signatures are designed to feel familiar if you already use `purrr`.

### Basic Examples

Count vertices in each structure:

    vertex_counts <- smap_int(large_struc, igraph::vcount)
    summary(vertex_counts)
    #>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
    #>     2.0     2.0     3.0     3.4     5.0     5.0

Find structures with more than 4 vertices:

    has_many_vertices <- smap_lgl(large_struc, ~ igraph::vcount(.x) > 4)
    sum(has_many_vertices)
    #> [1] 2000

Get the degree sequence of each structure:

    degree_sequences <- smap(large_struc, ~ igraph::degree(.x))
    degree_sequences[1:3]
    #> [[1]]
    #> 1 2 3 4 5
    #> 1 1 3 2 1
    #>
    #> [[2]]
    #> 1 2
    #> 1 1
    #>
    #> [[3]]
    #> 1 2 3
    #> 1 1 2

Check if any structure has isolated vertices:

    ssome(large_struc, ~ any(igraph::degree(.x) == 0))
    #> [1] FALSE

Verify all structures are connected:

    severy(large_struc, ~ igraph::is_connected(.x))
    #> [1] TRUE

### Beyond Basic `smap()`

Quick examples of the extended family:

    # smap2: Apply function with additional parameters
    thresholds <- c(3, 4, 5)
    large_enough <- smap2_lgl(struc[1:3], thresholds, function(g, threshold) {
      igraph::vcount(g) >= threshold
    })
    large_enough
    #> [1]  TRUE FALSE FALSE

    # simap: Include position information
    indexed_report <- simap_chr(large_struc[1:3], function(g, i) {
      paste0("#", i, ": ", igraph::vcount(g), " vertices")
    })
    indexed_report
    #> [1] "#1: 5 vertices" "#2: 2 vertices" "#3: 3 vertices"

Performance note: `simap` functions do not benefit from the unique structure optimization. Since each element has a different index, the combination of `(structure, index)` is always unique, breaking the deduplication that makes other `smap` functions fast. Use `simap` only when you truly need position information.

## Performance

The main performance benefit of `smap` functions comes from automatic deduplication:

    # Create a large dataset with high redundancy
    huge_struc <- rep(struc, 5000)  # 25,000 structures, only 5 unique

    cat("Dataset size:", length(huge_struc), "structures\n")
    #> Dataset size: 25000 structures
    cat("Unique structures:", length(attr(huge_struc, "structures")), "\n")
    #> Unique structures: 0
    cat("Redundancy factor:", length(huge_struc) / length(attr(huge_struc, "structures")), "x\n")
    #> Redundancy factor: Inf x

    library(tictoc)

    # Optimized approach: smap only processes 5 unique structures
    tic("smap_int (optimized)")
    vertex_counts_optimized <- smap_int(huge_struc, igraph::vcount)
    toc()
    #> smap_int (optimized): 0.001 sec elapsed

    # Naive approach: extract all graphs and process each one
    tic("Naive approach (all graphs)")
    all_graphs <- get_structure_graphs(huge_struc)  # Extracts all 25,000 graphs
    vertex_counts_naive <- purrr::map_int(all_graphs, igraph::vcount)
    toc()
    #> Naive approach (all graphs): 0.086 sec elapsed

    # Verify results are equivalent (though data types may differ)
    all.equal(vertex_counts_optimized, vertex_counts_naive)
    #> [1] TRUE

The higher the redundancy, the larger the performance gain. In real glycoproteomics datasets with repeated structures, this optimization can provide about 10x speedups.

## Additional Patterns

### Working with Complex Functions

The function you pass to `smap` must accept an `igraph` object as its first argument. You can use purrr-style lambda notation:

    # Calculate clustering coefficient for each structure
    clustering_coeffs <- smap_dbl(large_struc, ~ igraph::transitivity(.x, type = "global"))
    summary(clustering_coeffs)
    #>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
    #>       0       0       0       0       0       0    2000

### Combining Multiple Metrics

    # Create a compact structure summary.
    structure_analysis <- smap(large_struc, function(g) {
      list(
        vertices = igraph::vcount(g),
        edges = igraph::ecount(g),
        diameter = ifelse(igraph::is_connected(g), igraph::diameter(g), NA),
        clustering = igraph::transitivity(g, type = "global")
      )
    })

    # Convert to a more usable format
    analysis_df <- do.call(rbind, lapply(structure_analysis, data.frame))
    head(analysis_df)
    #>   vertices edges diameter clustering
    #> 1        5     4        3          0
    #> 2        2     1        1        NaN
    #> 3        3     2        1          0
    #> 4        5     4        2          0
    #> 5        2     1        1        NaN
    #> 6        5     4        3          0

### Memory-Efficient Filtering

    # Find only structures with exactly 5 vertices
    has_five_vertices <- smap_lgl(large_struc, ~ igraph::vcount(.x) == 5)
    five_vertex_structures <- large_struc[has_five_vertices]

    cat("Found", sum(has_five_vertices), "structures with exactly 5 vertices\n")
    #> Found 2000 structures with exactly 5 vertices

## When to Use `smap` Functions

Use `smap` functions when:

- You need to apply `igraph`-based functions to glycan structures.
- You want better performance with datasets containing repeated structures.
- You are building custom glycan analysis pipelines.

Use regular R functions when:

- You are working with compositions.
- You are operating on string representations.

Special note on `simap`:

While `simap` functions are convenient for position-aware operations, they do not provide performance benefits over regular `imap` functions. The inclusion of index information breaks the unique structure optimization, making each `(structure, index)` pair unique even when structures are identical.

## Example: Custom Motif Detection

Here’s how you might build a custom glycan analysis pipeline using `smap` functions:

    # Custom motif detector
    detect_branching <- function(g) {
      degrees <- igraph::degree(g)
      any(degrees >= 3)
    }

    # Apply to a large dataset using unique structure optimization.
    has_branching <- smap_lgl(large_struc, detect_branching)
    cat("Structures with branching:", sum(has_branching), "out of", length(large_struc), "\n")
    #> Structures with branching: 2000 out of 5000

    # Use smap2 to check structures against complexity thresholds
    complexity_thresholds <- rep(c(3, 4, 5, 2, 4), 1000)  # Thresholds for each structure
    meets_threshold <- smap2_lgl(large_struc, complexity_thresholds, function(g, threshold) {
      igraph::vcount(g) >= threshold
    })
    cat("Structures meeting complexity threshold:", sum(meets_threshold), "out of", length(large_struc), "\n")
    #> Structures meeting complexity threshold: 2000 out of 5000

## Summary

The `smap` family provides structure-aware mapping functions for glycan structure vectors. It lets you write custom graph-based analyses while preserving the unique structure optimization used by `glyrepr`.

Key takeaways:

- Unique structure optimization stores repeated structures efficiently.
- `smap` functions are `purrr`-like tools that understand glycan structure vectors.
- Performance gains are strongest when datasets contain repeated structures.
- Use `smap` for structures, and use regular R or `purrr` functions for other data types.

## Session Information

    sessionInfo()
    #> R version 4.5.1 (2025-06-13)
    #> Platform: aarch64-apple-darwin20
    #> Running under: macOS Tahoe 26.3.1
    #>
    #> Matrix products: default
    #> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
    #> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    #>
    #> locale:
    #> [1] C/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
    #>
    #> time zone: Asia/Shanghai
    #> tzcode source: internal
    #>
    #> attached base packages:
    #> [1] stats     graphics  grDevices utils     datasets  methods   base
    #>
    #> other attached packages:
    #> [1] tictoc_1.2.1   lobstr_1.1.3   dplyr_1.2.1    tibble_3.3.1   purrr_1.2.2
    #> [6] glyrepr_0.11.0
    #>
    #> loaded via a namespace (and not attached):
    #>  [1] jsonlite_2.0.0    compiler_4.5.1    tidyselect_1.2.1  stringr_1.6.0
    #>  [5] jquerylib_0.1.4   yaml_2.3.12       fastmap_1.2.0     R6_2.6.1
    #>  [9] generics_0.1.4    igraph_2.2.3      knitr_1.51        backports_1.5.1
    #> [13] checkmate_2.3.4   rstackdeque_1.1.1 bslib_0.9.0       pillar_1.11.1
    #> [17] rlang_1.2.0       utf8_1.2.6        cachem_1.1.0      stringi_1.8.7
    #> [21] xfun_0.55         sass_0.4.10       otel_0.2.0        cli_3.6.6
    #> [25] magrittr_2.0.5    digest_0.6.39     lifecycle_1.0.5   prettyunits_1.2.0
    #> [29] vctrs_0.7.3       evaluate_1.0.5    glue_1.8.0        rmarkdown_2.30
    #> [33] tools_4.5.1       pkgconfig_2.0.3   htmltools_0.5.9