161 distributed fails at some nset values

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: CoGAPS
-Version: 3.33.1
+Version: 3.33.2
 Date: 2025-03-11
 Title: Coordinated Gene Activity in Pattern Sets
 Author: Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey,

R/DistributedCogaps.R

@@ -247,8 +247,8 @@ stitchTogether <- function(result, allParams, sets)
             if (identical(sort(indices), sort(setIndices)))
             {
                 reorder <- match(indices, setIndices)
-                Amean <- Amean[reorder,]
-                Asd <- Asd[reorder,]
+                Amean <- Amean[reorder,,drop=FALSE]
+                Asd <- Asd[reorder,,drop=FALSE]
             }
         }
     }
@@ -269,8 +269,8 @@ stitchTogether <- function(result, allParams, sets)
             if (identical(sort(indices), sort(setIndices)))
             {
                 reorder <- match(indices, setIndices)
-                Pmean <- Pmean[reorder,]
-                Psd <- Psd[reorder,]
+                Pmean <- Pmean[reorder,,drop=FALSE]
+                Psd <- Psd[reorder,,drop=FALSE]
             }
         }
     }

tests/testthat/test_DistributedCogaps.R

@@ -44,4 +44,30 @@ test_that("featureLoadings and sampleFactors are not all 0s in genome-wide", {
   expect_true(sort((dim(featureLoadings)))[1] == params@nPatterns)
   expect_true(sort((dim(sampleFactors)))[2] == ncol(GIST.matrix))
   expect_true(sort((dim(featureLoadings)))[2] == nrow(GIST.matrix))
+})
+
+# One consensus pattern makes the stitched matrices one column wide. Without
+# drop=FALSE the re-ordering in stitchTogether turned them into vectors, whose
+# rownames are NULL, and the run died with "no gene names given".
+test_that("a one-pattern distributed run keeps its dim names", {
+  data(GIST)
+  for (mode in c("genome-wide", "single-cell"))
+  {
+    params <- CogapsParams(seed=42,
+                           nIterations = 100,
+                           nPatterns = 1,
+                           sparseOptimization = as.logical(0),
+                           distributed = mode)
+    params <- setDistributedParams(params, nSets = 2)
+    cg <- CoGAPS(GIST.matrix, params=params)
+
+    expect_true(is.matrix(cg@featureLoadings))
+    expect_true(is.matrix(cg@sampleFactors))
+    expect_equal(ncol(cg@featureLoadings), 1L)
+    expect_equal(ncol(cg@sampleFactors), 1L)
+    expect_equal(nrow(cg@featureLoadings), nrow(GIST.matrix))
+    expect_equal(nrow(cg@sampleFactors), ncol(GIST.matrix))
+    expect_false(is.null(rownames(cg@featureLoadings)))
+    expect_false(is.null(rownames(cg@sampleFactors)))
+  }
 })