Ensure multiple precomputed neighbor data all has the same n_neighbors.

jlmelville · Dec 6, 2018 · 157abba · 157abba
1 parent c93adcf
commit 157abba
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Showing 2 changed files with 22 additions and 6 deletions.
diff --git a/R/uwot.R b/R/uwot.R
@@ -1191,6 +1191,12 @@ data2set <- function(X, Xcat, n_neighbors, metrics, nn_method,
     # Extract this block of nn data from list of lists
     if (metric == "precomputed") {
       nn_sub <- nn_method[[i]]
+      if (i == 1) {
+        n_neighbors <- NULL
+      }
+      else {
+        n_neighbors <- ncol(nn_method[[1]]$idx)
+      }
     }
 
     x2set_res <- x2set(Xsub, n_neighbors, metric, nn_method = nn_sub,
@@ -1229,7 +1235,9 @@ x2nn <- function(X, n_neighbors, metric, nn_method,
                  n_vertices = x2nv(X),
                  verbose = FALSE) {
   if (is.list(nn_method)) {
-    validate_nn(nn_method, n_vertices)
+    # on first iteration n_neighbors is NULL
+    # on subsequent iterations ensure n_neighbors is consistent for all data
+    validate_nn(nn_method, n_vertices, n_neighbors = n_neighbors)
     nn <- nn_method
   }
   else {
@@ -1254,16 +1262,19 @@ x2nn <- function(X, n_neighbors, metric, nn_method,
   nn
 }
 
-validate_nn <- function(nn_method, n_vertices) {
+validate_nn <- function(nn_method, n_vertices, n_neighbors = NULL) {
   if (!is.matrix(nn_method$idx)) {
     stop("Couldn't find precalculated 'idx' matrix")
   }
   if (nrow(nn_method$idx) != n_vertices) {
-    stop("Precalculated 'idx' matrix must have ", n_vertices, " rows, but
-           found ", nrow(nn_method$idx))
+    stop("Precalculated 'idx' matrix must have ", n_vertices, 
+         " rows, but found ", nrow(nn_method$idx))
+  }
+
+  # set n_neighbors from these matrices if it hasn't been already set
+  if (is.null(n_neighbors)) {
+    n_neighbors <- ncol(nn_method$idx)
   }
-  n_neighbors <- ncol(nn_method$idx)
-
   if (!is.matrix(nn_method$dist)) {
     stop("Couldn't find precalculated 'dist' matrix")
   }

diff --git a/tests/testthat/test_errors.R b/tests/testthat/test_errors.R
@@ -24,3 +24,8 @@ expect_error(lvish(iris10, n_threads = 0, perplexity = 50), "perplexity")
 expect_error(umap(iris10, n_threads = 0, n_neighbors = 4, y = c(1:9, NA)), "numeric y")
 expect_error(umap(X = NULL, n_threads = 0, n_neighbors = 4, nn_method = nn, 
                   init = "spca"), "spca")
+# add an extra column to nn
+nn5 <- nn
+nn5$idx <- cbind(nn5$idx, rep(100, nrow(nn5$idx)))
+nn5$dist <- cbind(nn5$dist, rep(100.0, nrow(nn5$dist)))
+expect_error(umap(X = NULL, n_threads = 0,  nn_method = list(nn, nn5)), "Precalculated")