#118 and #129 fix uwot_transform's fgraph dimensions

NEWS.md

@@ -2,8 +2,13 @@
 
 ## Bug fixes and minor improvements
 
-* Setting `num_threads` directly in `umap2` did not result in the sgd threads
-being updated to that value when `batch = TRUE`, which it should have been.
+* Setting `num_threads` directly in `umap2` did not result in the number of SGD
+threads being updated to that value when `batch = TRUE`, which it should have
+been.
+* Despite assertions to the contrary in version 0.2.1, `umap_transform`
+continued to return the fuzzy graph in transposed form. Thank you
+[PedroMilanezAlmeida](https://github.com/PedroMilanezAlmeida) for 
+reopening the issue (<https://github.com/jlmelville/uwot/issues/118>).
 
 # uwot 0.2.2
 

R/transform.R

@@ -832,6 +832,11 @@ umap_transform <- function(X = NULL, model = NULL,
     res <- list(embedding = embedding)
     for (name in ret_extra) {
       if (name == "fgraph") {
+        if (batch) {
+          # #129: we transposed graph in the batch=TRUE case (#118) but need to
+          # transpose back for export
+          graph <- Matrix::t(graph)
+        }
         res$fgraph <- graph
       }
       if (name == "sigma") {

tests/testthat/test_transform.R

@@ -406,5 +406,33 @@ test_that("graph dim is consistent when n_epochs = 0", {
     dim(iris_transform_10$fgraph),
     dim(iris_transform_0$fgraph)
   )
-  expect_equal(dim(iris_transform_10$fgraph), c(100, 50))
+  expect_equal(dim(iris_transform_10$fgraph), c(50, 100))
+
+
+  #118/129 and also without batch
+  iris_model_no_batch <-
+    umap(
+      iris_species_12,
+      ret_model = TRUE,
+      n_epochs = 0,
+      batch = FALSE
+    )
+
+  iris_transform_10_no_batch <- umap_transform(iris_species_3,
+                                      iris_model_no_batch,
+                                      n_epochs = 10,
+                                      ret_extra = "fgraph"
+  )
+
+  iris_transform_0_no_batch <- umap_transform(iris_species_3,
+                                     iris_model_no_batch,
+                                     n_epochs = 0,
+                                     ret_extra = "fgraph"
+  )
+
+  expect_equal(
+    dim(iris_transform_10_no_batch$fgraph),
+    dim(iris_transform_0_no_batch$fgraph)
+  )
+  expect_equal(dim(iris_transform_10_no_batch$fgraph), c(50, 100))
 })