tests for ambiguity

tests/testthat/test_translate.R

@@ -0,0 +1,86 @@
+#!/usr/bin/env Rscript
+
+#
+#  This file is part of the `OmnipathR` R package
+#
+#  Copyright
+#  2018-2024
+#  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
+#
+#  File author(s): Alberto Valdeolivas
+#                  Dénes Türei ([email protected])
+#                  Attila Gábor
+#
+#  Distributed under the MIT (Expat) License.
+#  See accompanying file `LICENSE` or find a copy at
+#      https://directory.fsf.org/wiki/License:Expat
+#
+#  Website: https://r.omnipathdb.org/
+#  Git repo: https://github.com/saezlab/OmnipathR
+#
+
+library(OmnipathR)
+library(tibble)
+library(dplyr)
+library(magrittr)
+library(tidyselect)
+
+
+omnipath_set_console_loglevel('fatal')
+
+input0 <- tibble(
+    a = c('A', 'A', 'A', 'B', 'C', 'D', 'E'),
+    b = c('a', 'b', 'c', 'd', 'a', 'e', 'e')
+)
+
+input1 <-
+    input0 %>%
+    group_by(a) %>%
+    mutate(b = list(b)) %>%
+    summarize_all(~extract(., 1L))
+
+output_expanded <- tibble(
+    a = c('A', 'A', 'A', 'B', 'C', 'D', 'E'),
+    b = c('a', 'b', 'c', 'd', 'a', 'e', 'e'),
+    a_b_to_ambiguity = c(3L, 3L, 3L, 1L, 1L, 1L, 1L),
+    a_b_from_ambiguity = c(2L, 1L, 1L, 1L, 2L, 2L, 2L),
+    a_b_ambiguity = c(
+        'many-to-many',
+        'one-to-many',
+        'one-to-many',
+        'one-to-one',
+        'many-to-one',
+        'many-to-one',
+        'many-to-one'
+    )
+)
+
+output_collapsed <-
+    output_expanded %>%
+    group_by(a) %>%
+    reframe(across(everything(), ~list(.x))) %>%
+    ungroup %>%
+    rowwise %>%
+    mutate(across(ends_with('ambiguity'), ~list(set_names(.x, b)))) %>%
+    ungroup
+
+
+test_that(
+    'Translation ambiguity [expand-expanded]',
+    expect_equal(output_expanded, ambiguity(input0, a, b))
+)
+
+test_that(
+    'Translation ambiguity [expand-collapsed]',
+    expect_equal(output_expanded, ambiguity(input1, a, b, expand = TRUE))
+)
+
+test_that(
+    'Translation ambiguity [collapse-expanded]',
+    expect_equal(output_collapsed, ambiguity(input0, a, b, expand = FALSE))
+)
+
+test_that(
+    'Translation ambiguity [collapse-collapsed]',
+    expect_equal(output_collapsed, ambiguity(input1, a, b))
+)