dimReds updates

NAMESPACE

@@ -54,6 +54,7 @@ export("datasets<-")
 export("defaultCluster<-")
 export("defaultDimRed<-")
 export("dimRed<-")
+export("dimReds<-")
 export("featureMeta<-")
 export("h5fileInfo<-")
 export("normData<-")
@@ -84,6 +85,7 @@ export(datasets)
 export(defaultCluster)
 export(defaultDimRed)
 export(dimRed)
+export(dimReds)
 export(downsample)
 export(exportInteractTrack)
 export(featureMeta)
@@ -210,6 +212,7 @@ exportMethods("datasets<-")
 exportMethods("defaultCluster<-")
 exportMethods("defaultDimRed<-")
 exportMethods("dimRed<-")
+exportMethods("dimReds<-")
 exportMethods("dimnames<-")
 exportMethods("featureMeta<-")
 exportMethods("h5fileInfo<-")
@@ -230,6 +233,7 @@ exportMethods(defaultCluster)
 exportMethods(defaultDimRed)
 exportMethods(dim)
 exportMethods(dimRed)
+exportMethods(dimReds)
 exportMethods(dimnames)
 exportMethods(featureMeta)
 exportMethods(getH5File)

R/classConversion.R

@@ -137,7 +137,7 @@ as.liger.Seurat <- function(
     for (rd in SeuratObject::Reductions(object)) {
         mat <- object[[rd]][[]]
         colnames(mat) <- seq_len(ncol(mat))
-        cellMeta(lig, rd) <- mat
+        dimRed(lig, rd) <- mat
     }
     return(lig)
 }
@@ -341,29 +341,14 @@ ligerToSeurat <- function(
     }
 
     # Split normal data.frame compatible info and dimReds
-    metadata <- data.frame(row.names = colnames(object))
-    dimReds <- list()
-    for (i in seq_along(cellMeta(object))) {
-        varname <- names(cellMeta(object))[i]
-        var <- cellMeta(object)[[i]]
-        if (is.null(dim(var))) metadata[[varname]] <- var
-        else dimReds[[varname]] <- var
-    }
+    metadata <- .DataFrame.as.data.frame(cellMeta(object))
+    dimReds <- dimReds(object)
     srt <- Seurat::CreateSeuratObject(counts = Assay, assay = assay,
                                       meta.data = metadata)
 
     srt$orig.ident <- orig.ident
     Seurat::Idents(srt) <- idents
 
-    # if (!is.null(data)) {
-    #     srt <- .setSeuratData(srt, layer = "ligerNormData", slot = "data",
-    #                           value = data, assay = assay, denseIfNeeded = FALSE)
-    # }
-    # if (!is.null(scale.data)) {
-    #     srt <- .setSeuratData(srt, layer = "ligerScaleData", slot = "scale.data",
-    #                           value = scale.data, assay = assay,
-    #                           denseIfNeeded = TRUE)
-    # }
     # Attempt to get H.norm primarily. If it is NULL, then turn to H
     h <- getMatrix(object, "H.norm") %||%
         getMatrix(object, "H", returnList = TRUE)

R/generics.R

@@ -276,6 +276,20 @@ setGeneric(
 #' default cluster labeling, we also constructed the feature of default dimRed.
 #' It can be set with \code{defaultDimRed(obj) <- "existingMatLikeVar"} and the
 #' matrix can be retrieved with \code{defaultDimRed(obj)}.
+setGeneric(
+    "dimReds",
+    function(x) standardGeneric("dimReds")
+)
+
+#' @export
+#' @rdname liger-class
+setGeneric(
+    "dimReds<-",
+    function(x, value) standardGeneric("dimReds<-")
+)
+
+#' @export
+#' @rdname liger-class
 setGeneric(
     "dimRed",
     function(x, name = NULL, useDatasets = NULL, cellIdx = NULL, ...) {

R/liger-methods.R

@@ -1125,6 +1125,26 @@ setReplaceMethod(
     }
 )
 
+#' @export
+#' @rdname liger-class
+setMethod(
+    "dimReds",
+    signature = c(x = "liger"),
+    function(x) x@dimReds
+)
+
+#' @export
+#' @rdname liger-class
+setReplaceMethod(
+    "dimReds",
+    signature(x = "liger", value = "list"),
+    function(x, value) {
+        x@dimReds <- value
+        validObject(x)
+        return(x)
+    }
+)
+
 #' @export
 #' @rdname liger-class
 setMethod(

R/util.R

@@ -685,7 +685,7 @@ searchH <- function(object, useRaw = NULL) {
 # use when you have objects created when this package was named by `rliger2`
 # 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 = NULL) {
+rliger2_to_rliger_namespace <- function(obj, dimredName) {
     cm <- obj@cellMeta
     drList <- list()
     for (i in dimredName) {