summarize_semtypes {rsemmed} | R Documentation

## Summarize semantic types

### Description

Summarize the semantic types present in a collection of nodes

### Usage

    summarize_semtypes(graph, object, print = TRUE, is_path = TRUE)

### Arguments

`graph` | The SemMed graph
`object` | A vertex sequence (`igraph.vs`), a list of vertex sequences, or a list of vertex sequence lists
`print` | If `TRUE`, information on semantic types will be printed to the screen.
`is_path` | If `TRUE`, `object` contains paths (ordered sequences of nodes).

### Details

`summarize_semtypes` summarizes the semantic types present in supplied node collections and has different behavior depending on whether the node collection is ordered (paths) or unordered. Using `is_path = TRUE` indicates that the nodes are ordered. Using `is_path = FALSE` indicates that the nodes are an unordered collection, often from `find_nodes` or `grow_nodes`.

Using `is_path = TRUE`: When the node collection is ordered, the object is assumed to be the result of `find_paths` or a subset of such an object. Because `find_paths` returns a list of paths lists, `summarize_semtypes` takes a single path, a list of paths, or a list of path lists as input. In the case of a collection of ordered nodes, `summarize_semtypes` counts the semantic types present in `object`. If a node is associated with multiple semantic types, each type is counted once. The first and last nodes of each path are removed they correspond to the nodes in `from` and `to` from `find_paths`, and it is assumed that the middle nodes on the paths are more of interest. The tabulations are printed to screen (if `print = TRUE`) and returned as `table`'s. These `table`'s are bundled into a list-column of a `tbl` in the (invisbly returned) output. Each row of the `tbl` corresponds to a `from`-`to` pair present in `object`.

Using `is_path = FALSE`: This option is for summarizing results from `find_nodes` and `grow_nodes`, which return unordered node sets. (Note: paths and unordered node sets are both represented as `igraph` vertex sequences (class `igraph.vs`).) The printed output shows information for each semantic type present in `object`. It shows all nodes of that semantic type as well as their degree and degree percentile within the entire `graph`. The (invisibly returned) output combines all of the printed information in a `tbl`.

### Value

Output is returned invisibly. If `is_path = TRUE`, a `tbl` where each row corresponds to a `from`-`to` pair in `object`. The last column is a list-column containing `table`'s of semantic type counts. If `is_path = FALSE`, a `tbl` where each row corresponds to a name-semantic type combination. Columns give node name, semantic type, degree, and degree percentile.

### See Also

`summarize_predicates` for summarizing predicates on edges

`find_paths` for searching for paths between node sets

`find_nodes` and `grow_nodes` for searching for and filtering nodes

### Examples

    data(g_mini)

    node_cortisol <- find_nodes(g_mini, "Serum cortisol")
    node_stress <- find_nodes(g_mini, "Chronic Stress")
    paths <- find_paths(g_mini, from = node_cortisol, to = node_stress)
    summarize_semtypes(g_mini, paths)

    nodes_mood <- find_nodes(g_mini, "mood")
    summarize_semtypes(g_mini, nodes_mood, is_path = FALSE)

[Package rsemmed version 1.0.0 Index]