Added switch to sequential processing when cl = 1

PixelgenTechnologies · Aug 15, 2024 · 8190d34 · 8190d34
1 parent d6e89ae
commit 8190d34
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Showing 4 changed files with 27 additions and 8 deletions.
diff --git a/R/differential_colocalization_analysis.R b/R/differential_colocalization_analysis.R
@@ -134,13 +134,14 @@ RunDCA.data.frame <- function(
     # Use sequential processing when cl is 1
     if (cl == 1) {
       chunks <- seq_along(test_groups)
-    }
-    # Parallel processing when cl is the number of child processes
-    if ((length(test_groups) * cl) > (cl * 100)) {
-      # Cut into even chunks of 100 values in each chunk
-      chunks <- ceiling(seq_along(test_groups) / 100)
     } else {
-      chunks <- cut(seq_along(test_groups), cl)
+      # Parallel processing when cl is the number of child processes
+      if ((length(test_groups) * cl) > (cl * 100)) {
+        # Cut into even chunks of 100 values in each chunk
+        chunks <- ceiling(seq_along(test_groups) / 100)
+      } else {
+        chunks <- cut(seq_along(test_groups), cl)
+      }
     }
   } else {
     # Sequential processing when cl is NULL

diff --git a/R/differential_polarity_analysis.R b/R/differential_polarity_analysis.R
@@ -150,9 +150,10 @@ RunDPA.data.frame <- function(
     # Use sequential processing when cl is 1
     if (cl == 1) {
       chunks <- seq_along(test_groups)
+    } else {
+      # Parallel processing when cl is the number of child processes
+      chunks <- cut(seq_along(test_groups), cl)
     }
-    # Parallel processing when cl is the number of child processes
-    chunks <- cut(seq_along(test_groups), cl)
   } else {
     # Sequential processing when cl is NULL
     chunks <- seq_along(test_groups)

diff --git a/tests/testthat/test-RunDCA.R b/tests/testthat/test-RunDCA.R
@@ -21,6 +21,7 @@ seur_merged <- merge(seur1, seur2, add.cell.ids = c("Sample1", "Sample2"))
 seur_merged <- subset(seur_merged, features = c("ACTB", "HLA-ABC"))
 
 test_that("RunDCA works as expected on a data.frame and that ColocalizationHeatmap works on the output", {
+
   expect_no_error(suppressWarnings(dca_markers <- RunDCA(colocalization_table_merged,
     contrast_column = "sample",
     targets = "Sample1", reference = "Sample2"
@@ -63,6 +64,13 @@ test_that("RunDCA works as expected on a data.frame and that ColocalizationHeatm
 
   expect_equal(dca_markers[1:2, ], expected_result)
 
+  # cl = 1 should witch to sequential processing
+  expect_no_error(suppressWarnings(dca_markers <- RunDCA(colocalization_table_merged,
+                                                         contrast_column = "sample",
+                                                         targets = "Sample1", reference = "Sample2",
+                                                         cl = 1
+  )))
+
   # Colocalization heatmap
   expect_no_error(p_heatmap <- ColocalizationHeatmap(dca_markers))
   expect_s3_class(p_heatmap, "pheatmap")

diff --git a/tests/testthat/test-RunDPA.R b/tests/testthat/test-RunDPA.R
@@ -18,6 +18,7 @@ seur2$sample <- "Sample2"
 seur_merged <- merge(seur1, seur2, add.cell.ids = c("Sample1", "Sample2"))
 
 test_that("RunDPA works as expected on a data.frame", {
+
   # morans_z
   expect_no_error(suppressWarnings(dpa_markers <- RunDPA(polarization_table_merged,
     contrast_column = "sample",
@@ -115,6 +116,14 @@ test_that("RunDPA works as expected on a data.frame", {
 
   # Automatic selection of targets
   expect_no_error(suppressWarnings(dpa_markers <- RunDPA(seur_merged, contrast_column = "sample", reference = "Sample2")))
+
+  # cl = 1 should witch to sequential processing
+  expect_no_error(suppressWarnings(dpa_markers <- RunDPA(seur_merged,
+                                                         contrast_column = "sample",
+                                                         targets = "Sample1", reference = "Sample2",
+                                                         cl = 1
+  )))
+
 })
 
 test_that("RunDPA works as expected on a Seurat object", {