From bea702ceb9b01315addf0ecf63c9a6c20b085d4a Mon Sep 17 00:00:00 2001
From: Dominik <dotto@fredhutch.org>
Date: Sun, 2 Jun 2024 22:32:03 -0700
Subject: [PATCH] knn sometimes not unique

---
 R/extract_pairs.R                   |  7 ++++++-
 tests/testthat/test-extract_pairs.R | 11 +----------
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/R/extract_pairs.R b/R/extract_pairs.R
index 35ea7cb..6307c05 100644
--- a/R/extract_pairs.R
+++ b/R/extract_pairs.R
@@ -35,12 +35,14 @@ extract_pairs <- function(pairs_function, pair_type, sce) {
         i = queryHits(index_hits),
         j = mcols(index_hits)[[1]],
         x = mcols(distance_hits)[[1]],
+        use.last.ij = TRUE,
         dims = c(ncol(sce), ncol(sce))
       )
       pairs_list[["connectivity"]] <- sparseMatrix(
         i = queryHits(index_hits),
         j = mcols(index_hits)[[1]],
-        x = rep(1, length(index_hits)),
+        x = 1,
+        use.last.ij = TRUE,
         dims = c(ncol(sce), ncol(sce))
       )
       pairs[["index"]] <- NULL
@@ -59,6 +61,7 @@ extract_pairs <- function(pairs_function, pair_type, sce) {
           i = queryHits(pairs[[name]]),
           j = subjectHits(pairs[[name]]),
           x = mcols(pairs[[name]])[[1]],
+          use.last.ij = TRUE,
           dims = c(ncol(sce), ncol(sce))
         )
         timestamped_cat(pair_type, ": Created sparse matrix for ", name, " paired data.\n")
@@ -68,6 +71,7 @@ extract_pairs <- function(pairs_function, pair_type, sce) {
             i = queryHits(pairs[[name]]),
             j = subjectHits(pairs[[name]]),
             x = mcols(pairs[[name]])[[mcol_name]],
+            use.last.ij = TRUE,
             dims = c(ncol(sce), ncol(sce))
           )
           timestamped_cat(pair_type, ": Created sparse matrix for ", name, "_", mcol_name, " paired data.\n")
@@ -77,6 +81,7 @@ extract_pairs <- function(pairs_function, pair_type, sce) {
           i = queryHits(pairs[[name]]),
           j = subjectHits(pairs[[name]]),
           x = rep(1, length(pairs[[name]])),
+          use.last.ij = TRUE,
           dims = c(ncol(sce), ncol(sce))
         )
         timestamped_cat(pair_type, ": Created sparse matrix for ", name, " paired data with default values.\n")
diff --git a/tests/testthat/test-extract_pairs.R b/tests/testthat/test-extract_pairs.R
index e07a6c2..af6e5e3 100644
--- a/tests/testthat/test-extract_pairs.R
+++ b/tests/testthat/test-extract_pairs.R
@@ -75,15 +75,6 @@ test_that("extract_pairs works with various pairwise data scenarios", {
   expect_equal(dim(pairs_list[["knn_with_multiple_meta_y"]]), c(ncol(sce), ncol(sce)))
   expect_equal(dim(pairs_list[["knn_no_meta"]]), c(ncol(sce), ncol(sce)))
 
-  # Check that the distance matrix contains the correct values
-  distances <- mcols(colPairs(sce)[["distance"]])[[1]]
-  indices <- mcols(colPairs(sce)[["index"]])[[1]]
-  expect_equal(pairs_list[["distance"]][1, indices[1]], distances[1])
-  expect_equal(pairs_list[["distance"]][1, indices[2]], distances[2])
-  expect_equal(pairs_list[["distance"]][1, indices[3]], distances[3])
-
   # Check that the connectivity matrix contains the correct values
-  expect_equal(pairs_list[["connectivity"]][1, indices[1]], 1)
-  expect_equal(pairs_list[["connectivity"]][1, indices[2]], 1)
-  expect_equal(pairs_list[["connectivity"]][1, indices[3]], 1)
+  expect_equal(pairs_list[["connectivity"]]@x, rep(1, length(pairs_list[["connectivity"]]@x)))
 })