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Unnest Mapping

unnest_mapping.Rd

Tidies pyobo_map() results stored in the column of a data frame in two steps:

  1. Extracts mapping results from specialized ScoredMatch python objects (as defined by GILDA).

  2. Unnests the results (from list of data frames).

Usage

unnest_mapping(
  df,
  col,
  prefix = NULL,
  prefix_sep = ":",
  best_only = TRUE,
  warn_best_gt1 = FALSE,
  ...
)

Arguments

df

A data.frame.

col

The column with pyobo_map() results, as a tidy-select specification.

prefix

Optional prefix to add to namespace local unique identifiers (LUI; e.g. 4, the LUI for "disease" in DO), as a string; preferably to create a complete namespace ID (e.g. "DOID:4").

prefix_sep

Optional separator placed between prefix and namespace LUIs, as a string. Ignored if prefix = NULL.

best_only

Whether to return the best scoring result(s) only, as a boolean. FALSE will return all results. NOTE: TRUE will return more than one result in the case of ties.

warn_best_gt1

Whether to warn that best mapping ties exist for a term.

...

Arguments passed on to tidyr::unnest

keep_empty

By default, you get one row of output for each element of the list that you are unchopping/unnesting. This means that if there's a size-0 element (like NULL or an empty data frame or vector), then that entire row will be dropped from the output. If you want to preserve all rows, use keep_empty = TRUE to replace size-0 elements with a single row of missing values.

ptype

Optionally, a named list of column name-prototype pairs to coerce cols to, overriding the default that will be guessed from combining the individual values. Alternatively, a single empty ptype can be supplied, which will be applied to all cols.

names_sep

If NULL, the default, the outer names will come from the inner names. If a string, the outer names will be formed by pasting together the outer and the inner column names, separated by names_sep.

names_repair

Used to check that output data frame has valid names. Must be one of the following options:

  • "minimal": no name repair or checks, beyond basic existence,

  • "unique": make sure names are unique and not empty,

  • "check_unique": (the default), no name repair, but check they are unique,

  • "universal": make the names unique and syntactic

  • a function: apply custom name repair.

  • tidyr_legacy: use the name repair from tidyr 0.8.

  • a formula: a purrr-style anonymous function (see rlang::as_function())

See vctrs::vec_as_names() for more details on these terms and the strategies used to enforce them.

Value

The input data frame with additional columns id, term (namespace label), and score (mapping score as determined by GILDA). The data frame will have additional rows if best_score = FALSE or ties for best score exist for a term.