Merge branch 'master' into cinmf

welch-lab · Mar 31, 2024 · 4d203a4 · 4d203a4
2 parents 388b757 + 9c3dc07
commit 4d203a4
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Showing 2 changed files with 32 additions and 20 deletions.
diff --git a/R/import.R b/R/import.R
@@ -477,6 +477,9 @@ readLiger <- function(
     if (!inherits(obj, "liger")) # nocov start
         cli::cli_abort("Object is not of class {.cls liger}.") # nocov end
     ver <- obj@version
+    if (ver == package_version("1.99.0")) {
+        obj <- rliger2_to_rliger_namespace(obj, dimredName = dimredName)
+    }
     if (ver >= package_version("1.99.0")) {
         if (isH5Liger(obj)) obj <- restoreH5Liger(obj)
         return(obj)

diff --git a/R/util.R b/R/util.R
@@ -686,27 +686,18 @@ searchH <- function(object, useRaw = NULL) {
 # now we rename the package back to `rliger` and you'll need to have the objects
 # compatible with "new" package name.
 rliger2_to_rliger_namespace <- function(obj, dimredName) {
-    cm <- obj@cellMeta
+    # Slots that contain things of rliger2 namespace
+    datasetList <- list()
     drList <- list()
+    commandList <- list()
+
+    cm <- obj@cellMeta
     for (i in dimredName) {
         drList[[i]] <- cm[[i]]
         cm[[i]] <- NULL
     }
-    new <- methods::new(
-        "liger",
-        datasets = obj@datasets,
-        cellMeta = cm,
-        varFeatures = obj@varFeatures,
-        W = obj@W,
-        H.norm = obj@H.norm,
-        uns = obj@uns,
-        commands = obj@commands,
-        version = obj@version
-    )
-    for (i in dimredName) {
-        dimRed(new, i) <- drList[[i]]
-    }
-    for (i in seq_along(obj)) {
+
+    for (i in names(obj@datasets)) {
         ld <- obj@datasets[[i]]
         basics <- list(
             rawData = ld@rawData,
@@ -748,11 +739,12 @@ rliger2_to_rliger_namespace <- function(obj, dimredName) {
                 Class = "ligerDataset"
             ))
         }
-        new@datasets[[i]] <- do.call("new", basics)
+        datasetList[[i]] <- do.call("new", basics)
     }
-    for (i in seq_along(new@commands)) {
-        cmd <- new@commands[[i]]
-        new@commands[[i]] <- methods::new(
+
+    for (i in names(obj@commands)) {
+        cmd <- obj@commands[[i]]
+        commandList[[i]] <- methods::new(
             "ligerCommand",
             funcName = cmd@funcName,
             time = cmd@time,
@@ -763,5 +755,22 @@ rliger2_to_rliger_namespace <- function(obj, dimredName) {
             dependencyVersion = cmd@dependencyVersion
         )
     }
+
+    new <- methods::new(
+        "liger",
+        datasets = datasetList,
+        cellMeta = cm,
+        varFeatures = obj@varFeatures,
+        W = obj@W,
+        H.norm = obj@H.norm,
+        uns = obj@uns,
+        commands = commandList,
+        version = obj@version
+    )
+
+    for (i in dimredName) {
+        dimRed(new, i) <- drList[[i]]
+    }
+
     new
 }