ci: remove redundant workflow files (rhub.yaml and windows-check.yml)

R/generate_taxa_cladogram_single.R

@@ -207,8 +207,23 @@ generate_taxa_cladogram_single <- function(
   fix_link_frame <- link_frame
   fix_link_frame[[min_label]] <- stringr::str_replace_all(fix_link_frame[[min_label]], pattern = " |\\(|\\)", replacement = "_")
   fix_link_frame[[min_label]] <- stringr::str_replace_all(fix_link_frame[[min_label]], pattern = "\\.", replacement = "")
-  # Build phylogenetic tree
-  treex <- build_tree(fix_link_frame, level_seq)
+
+  # Check and use existing tree if available, otherwise build from taxonomy
+  if (!is.null(data.obj$tree)) {
+    tree <- data.obj$tree
+    # Ensure tree tips match our feature names
+    common_tips <- intersect(tree$tip.label, fix_link_frame[[min_label]])
+    if (length(common_tips) > 0) {
+      message("Using phylogenetic tree from data object.")
+      treex <- ape::keep.tip(tree, common_tips)
+    } else {
+      message("No matching tips found between phylogenetic tree and features. Using taxonomy-based tree instead.")
+      treex <- build_tree(fix_link_frame, level_seq)
+    }
+  } else {
+    message("Building taxonomy-based tree.")
+    treex <- build_tree(fix_link_frame, level_seq)
+  }
 
   # Join and process test results
   inputframe_linked <- join_frames(test.list, level_seq, link_frame)

tests/testthat/test-generate_taxa_cladogram_single.R

@@ -0,0 +1,123 @@
+test_that("generate_taxa_cladogram_single works with and without phylogenetic tree", {
+  # Create mock data objects with more realistic taxonomic structure
+  features <- paste0("ASV", 1:5)  # 使用简单的ASV标识符
+
+  # Create feature annotation data frame - 避免使用可能冲突的列名
+  feature.ann <- data.frame(
+    tax_Kingdom = rep("Bacteria", 5),
+    tax_Phylum = c("Firmicutes", "Firmicutes", "Bacteroidetes", "Bacteroidetes", "Proteobacteria"),
+    tax_Class = c("Bacilli", "Clostridia", "Bacteroidia", "Flavobacteriia", "Gammaproteobacteria"),
+    row.names = features,
+    stringsAsFactors = FALSE
+  )
+
+  # Create abundance matrix
+  feature.tab <- matrix(
+    rpois(50, lambda = 10),
+    nrow = 5,
+    ncol = 10,
+    dimnames = list(features, paste0("Sample", 1:10))
+  )
+
+  # Create metadata
+  meta.dat <- data.frame(
+    Group = rep(c("A", "B"), each = 5),
+    row.names = paste0("Sample", 1:10)
+  )
+
+  # Create base data object
+  data.obj.no.tree <- list(
+    feature.tab = feature.tab,
+    feature.ann = feature.ann,
+    meta.dat = meta.dat
+  )
+
+  # Create mock test results
+  test.list <- list(
+    tax_Phylum = list(
+      "A_vs_B" = data.frame(
+        Feature = unique(feature.ann$tax_Phylum),
+        Coefficient = rnorm(3),
+        P.Value = runif(3),
+        Adjusted.P.Value = runif(3)
+      )
+    ),
+    tax_Class = list(
+      "A_vs_B" = data.frame(
+        Feature = unique(feature.ann$tax_Class),
+        Coefficient = rnorm(5),
+        P.Value = runif(5),
+        Adjusted.P.Value = runif(5)
+      )
+    )
+  )
+
+  # Create data object with tree - 确保树的标签与特征完全匹配
+  library(ape)
+  tree <- ape::read.tree(text = paste0("(", paste(features, collapse = ","), ");"))
+  tree$edge.length <- rep(1, nrow(tree$edge))
+  # 添加必要的属性
+  tree$node.label <- paste0("Node", 1:(tree$Nnode))
+
+  data.obj.with.tree <- data.obj.no.tree
+  data.obj.with.tree$tree <- tree
+
+  # Test cases
+  suppressWarnings({
+    # Test case 1: Without tree
+    result_no_tree <- capture_messages({
+      plot.list.no.tree <- generate_taxa_cladogram_single(
+        data.obj = data.obj.no.tree,
+        test.list = test.list,
+        group.var = "Group",
+        feature.level = c("tax_Phylum", "tax_Class"),
+        color.group.level = "tax_Phylum"
+      )
+    })
+    expect_true(any(grepl("Building taxonomy-based tree", result_no_tree)))
+
+    # Test case 2: With tree
+    result_with_tree <- capture_messages({
+      plot.list.with.tree <- generate_taxa_cladogram_single(
+        data.obj = data.obj.with.tree,
+        test.list = test.list,
+        group.var = "Group",
+        feature.level = c("tax_Phylum", "tax_Class"),
+        color.group.level = "tax_Phylum"
+      )
+    })
+    cat("\nActual messages with tree:\n")
+    print(result_with_tree)
+
+    # Test case 3: With mismatched tree
+    mismatched_tree <- ape::read.tree(text = "(Wrong1,Wrong2,Wrong3,Wrong4,Wrong5);")
+    mismatched_tree$edge.length <- rep(1, nrow(mismatched_tree$edge))
+    data.obj.mismatched <- data.obj.no.tree
+    data.obj.mismatched$tree <- mismatched_tree
+
+    result_mismatched <- capture_messages({
+      plot.list.mismatched <- generate_taxa_cladogram_single(
+        data.obj = data.obj.mismatched,
+        test.list = test.list,
+        group.var = "Group",
+        feature.level = c("tax_Phylum", "tax_Class"),
+        color.group.level = "tax_Phylum"
+      )
+    })
+  })
+
+  # Basic checks
+  expect_type(plot.list.no.tree, "list")
+  expect_type(plot.list.with.tree, "list")
+  expect_type(plot.list.mismatched, "list")
+
+  # Check list contents
+  expect_true(all(sapply(plot.list.no.tree, function(x) inherits(x, "ggplot"))))
+  expect_true(all(sapply(plot.list.with.tree, function(x) inherits(x, "ggplot"))))
+  expect_true(all(sapply(plot.list.mismatched, function(x) inherits(x, "ggplot"))))
+
+  # Check list length
+  expect_length(plot.list.no.tree, 1)
+  expect_length(plot.list.with.tree, 1)
+  expect_length(plot.list.mismatched, 1)
+})