Merge pull request #188 from MangiolaLaboratory/fix_parallel_chains_for_pathfinder

If estimate and remove_outliers are calculated with different fit met…

Author: stemangiola

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sccomp
 Title: Tests differences in cell-type proportion for single-cell data, robust to outliers
-Version: 1.99.14
+Version: 1.99.15
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre"))
                   )

R/methods.R

@@ -733,11 +733,16 @@ sccomp_remove_outliers.sccomp_tbl = function(.estimate,
 
         create_intercept = FALSE
       )),
-    parallel_chains = ifelse(data_for_model$is_vb, 1, attr(.estimate , "fit")$num_chains()), 
+    parallel_chains = ifelse(
+      inference_method %in% c("variational", "pathfinder") | 
+        attr(.estimate , "fit") |> is("CmdStanPathfinder"),
+        1, 
+       attr(.estimate , "fit")$num_chains()
+      ), 
     threads_per_chain = cores
 
   )
-  
+
   # Free memory
   rm(.estimate)
 
@@ -823,7 +828,6 @@ sccomp_remove_outliers.sccomp_tbl = function(.estimate,
       ...
     )
 
-  
   rng2 =  mod_rng |> sample_safe(
     generate_quantities_fx,
     fit2$draws(format = "matrix"),
@@ -852,7 +856,7 @@ sccomp_remove_outliers.sccomp_tbl = function(.estimate,
       create_intercept = FALSE
 
     )),
-    parallel_chains = ifelse(data_for_model$is_vb, 1, fit2$num_chains()), 
+    parallel_chains = ifelse(inference_method %in% c("variational", "pathfinder"), 1, fit2$num_chains()), 
     threads_per_chain = cores
 
   )

tests/testthat/test-sccomp_.R

@@ -823,4 +823,59 @@ test_that("sample ID malformed", {
 
 })
 
+test_that("LOO", {
+  skip_cmdstan()
+  
+  library(loo)
+  
+  # Fit first model
+  model_with_factor_association = 
+    seurat_obj |>
+    sccomp_estimate( 
+      formula_composition = ~ type, 
+      .sample =  sample, 
+      .cell_group = cell_group, 
+      inference_method = "hmc",
+      enable_loo = TRUE
+    ) |> 
+    expect_no_error()
+  
+  # Fit second model
+  model_without_association = 
+    seurat_obj |>
+    sccomp_estimate( 
+      formula_composition = ~ 1, 
+      .sample =  sample, 
+      .cell_group = cell_group, 
+      inference_method = "hmc",
+      enable_loo = TRUE
+    ) |> 
+    expect_no_error()
+  
+  # Compare models
+  loo_compare(
+    attr(model_with_factor_association, "fit")$loo(),
+    attr(model_without_association, "fit")$loo()
+  ) |> 
+    suppressWarnings() |> 
+    expect_no_error()
+  
+})
+
+
+test_that("use two methods", {
+
+  skip_cmdstan()
+
+    seurat_obj |>
+    sccomp_estimate( 
+      formula_composition = ~ 1, 
+      .sample =  sample, 
+      .cell_group = cell_group, 
+      inference_method = "hmc"
+    ) |> 
+    sccomp_remove_outliers(inference_method = "pathfinder") |> 
+    expect_no_error()
+  
+})