test.R

add test of markovProbability

R/projectPseudotimeToCell.R

@@ -64,10 +64,10 @@
 projectPseudotimeToCell <- function(milo, pb_milo, term_states = NULL, pseudotime_key = "pseudotime", suffix = "") {
     if(is.null(term_states))
     {
-      if(is.null(metadata(pb_milo)$branch.tips))
+      if(is.null(metadata(pb_milo)$branch.tips)) # ncov start
       {
         abort("Parameter Error: Please provide term_state, which should align with parameter terminal_state in function markovProbability")
-      }
+      } # nocov end
       else
         term_states <- metadata(pb_milo)$branch.tips
     }

tests/testthat/test-markovProbability.R

@@ -0,0 +1,56 @@
+# Mock data for testing
+data(sce_vdj)
+sce_vdj <- setupVdjPseudobulk(sce_vdj,
+     already.productive = FALSE,
+     allowed_chain_status = c("Single pair", "Extra pair")
+ )
+
+# Build Milo Object
+set.seed(100)
+milo_object <- miloR::Milo(sce_vdj)
+milo_object <- miloR::buildGraph(milo_object, k = 50, d = 20, reduced.dim = "X_scvi")
+milo_object <- miloR::makeNhoods(milo_object, reduced_dims = "X_scvi", d = 20)
+
+# Construct Pseudobulked VDJ Feature Space
+pb.milo <- vdjPseudobulk(milo_object, col_to_take = "anno_lvl_2_final_clean")
+pb.milo <- scater::runPCA(pb.milo, assay.type = "Feature_space")
+
+# Define root and branch tips
+pca <- t(as.matrix(SingleCellExperiment::reducedDim(pb.milo, type = "PCA")))
+branch.tips <- c(189, 198) # which.min(pca[, 2]) and which.max(pca[, 2])
+names(branch.tips) <- c("CD8+T", "CD4+T")
+root <- 177 # which.max(pca[, 1])
+
+# Construct Diffusion Map
+dm <- destiny::DiffusionMap(t(pca), n_pcs = 50, n_eigs = 10)
+dif.pse <- destiny::DPT(dm, tips = c(root, branch.tips), w_width = 0.1)
+# Since the markovProbability will also run in test-projectPseudotimeToCell.R as setup, we only consider two special circumstances here.
+test_that("markovProbability works correctly with terminal states as NULL",{
+  pb.milo <- markovProbability(
+    milo = pb.milo,
+    diffusionmap = dm,
+    terminal_state = NULL,
+    diffusiontime = dif.pse[[paste0("DPT", root)]],
+    root_cell = root,
+    pseudotime_key = "pseudotime"
+  )
+  expect_true(is(pb.milo, "Milo"))
+  expect_true("pseudotime" %in% colnames(colData(pb.milo)))
+  expect_true(any(grep("terminal_state",colnames(colData(pb.milo)))))
+  expect_false(is.null(metadata(pb.milo)))
+})
+
+test_that("markovProbability works correctly with only one terminal state",{
+  pb.milo <- markovProbability(
+    milo = pb.milo,
+    diffusionmap = dm,
+    terminal_state = 189,
+    diffusiontime = dif.pse[[paste0("DPT", root)]],
+    root_cell = root,
+    pseudotime_key = "pseudotime"
+  )
+  expect_true(is(pb.milo, "Milo"))
+  expect_true("pseudotime" %in% colnames(colData(pb.milo)))
+  expect_true(any(grep("terminal_state",colnames(colData(pb.milo)))))
+  expect_false(is.null(metadata(pb.milo)))
+})