Use proxyC for both distance matrices

openproblems-bio · Oct 22, 2024 · 3168845 · 3168845
1 parent dc3adb6
commit 3168845
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/src/metrics/coranking/config.vsh.yaml b/src/metrics/coranking/config.vsh.yaml
@@ -104,7 +104,6 @@ engines:
       cran:
         - coRanking
         - proxyC
-        - parallelDist
 runners:
   - type: executable
   - type: nextflow

diff --git a/src/metrics/coranking/script.R b/src/metrics/coranking/script.R
@@ -31,10 +31,13 @@ if (any(is.na(X_emb))) {
   # TODO: should we use a different distance metric for the high_dim?
   # TODO: or should we subset to the HVG?
   message("Compute high-dimensional distances")
-  dist_highdim <- proxyC::dist(high_dim, method = "euclidean")
-  diag(dist_highdim) <- 0 # Force diagonal to be 0
+  dist_highdim <- proxyC::dist(
+    high_dim, method = "euclidean", diag = TRUE, drop0 = TRUE
+  )
   message("Compute embedding distances")
-  dist_emb <- parallelDist::parallelDist(as.matrix(X_emb))
+  dist_emb <- proxyC::dist(
+    X_emb, method = "euclidean", diag = TRUE, drop0 = TRUE
+  )
 
   message("Compute ranking matrices")
   rmat_highdim <- rankmatrix(dist_highdim, input = "dist")