Fix SpatiallyVariableFeatures.Assay & Introduce SVFInfo/SpatiallyVariableFeatures.StdAssay

NAMESPACE

@@ -257,15 +257,19 @@ S3method(ReorderIdent,Seurat)
 S3method(S4ToList,default)
 S3method(S4ToList,list)
 S3method(SVFInfo,Assay)
+S3method(SVFInfo,Assay5)
 S3method(SVFInfo,Seurat)
+S3method(SVFInfo,StdAssay)
 S3method(SetAssayData,Assay)
 S3method(SetAssayData,Seurat)
 S3method(SetAssayData,StdAssay)
 S3method(SetIdent,Seurat)
 S3method(Simplify,Molecules)
 S3method(Simplify,Spatial)
 S3method(SpatiallyVariableFeatures,Assay)
+S3method(SpatiallyVariableFeatures,Assay5)
 S3method(SpatiallyVariableFeatures,Seurat)
+S3method(SpatiallyVariableFeatures,StdAssay)
 S3method(StashIdent,Seurat)
 S3method(Stdev,DimReduc)
 S3method(Stdev,Seurat)

R/assay.R

@@ -878,9 +878,9 @@ SpatiallyVariableFeatures.Assay <- function(
     method <- selection.method
   }
   vf <- SVFInfo(object = object, method = method, status = TRUE)
-  vf <- vf[rownames(x = vf)[which(x = vf[, "variable"][, 1])], ]
+  vf <- vf[rownames(x = vf)[which(!is.na(x = vf[, "variable"]))], ]
   if (!is.null(x = decreasing)) {
-    vf <- vf[order(x = vf[, "rank"], decreasing = !decreasing), ]
+    vf <- vf[order(x = vf[, "rank"][, 1], decreasing = !decreasing), ]
   }
   return(rownames(x = vf)[which(x = vf[, "variable"][, 1])])
 }
@@ -911,12 +911,12 @@ SVFInfo.Assay <- function(
     EXPR = method,
     markvariogram = grep(
       pattern = "r.metric",
-      x = colnames(x = object[]),
+      x = colnames(x = object[[]]),
       value = TRUE
     ),
     moransi = grep(
-      pattern = 'moransi',
-      x = colnames(x = object[]),
+      pattern = 'MoransI',
+      x = colnames(x = object[[]]),
       value = TRUE
     ),
     abort(message = paste("Unknown method:", sQuote(x = method)))
@@ -925,7 +925,7 @@ SVFInfo.Assay <- function(
     expr = svf.info <- object[[vars]],
     error = function(e) {
       stop(
-        "Unable to find highly variable feature information for method '",
+        "Unable to find spatially variable feature information for method '",
         method,
         "'",
         call. = FALSE

R/assay5.R

@@ -1687,6 +1687,102 @@ VariableFeatures.Assay5 <- VariableFeatures.StdAssay
 #'
 "VariableFeatures<-.Assay5" <- `VariableFeatures<-.StdAssay`
 
+#' @rdname VariableFeatures
+#' @export
+#' @method SVFInfo StdAssay
+#'
+SVFInfo.StdAssay <- function(
+  object,
+  method = c("markvariogram", "moransi"),
+  status = FALSE,
+  selection.method = deprecated(),
+  ...
+) {
+  CheckDots(...)
+  if (is_present(arg = selection.method)) {
+    .Deprecate(
+      when = '5.0.0',
+      what = 'SVFInfo(selection.method = )',
+      with = 'SVFInfo(method = )'
+    )
+    method <- selection.method
+  }
+  method <- match.arg(arg = method)
+  vars <- switch(
+    EXPR = method,
+    markvariogram = grep(
+      pattern = "r.metric",
+      x = colnames(x = object[[]]),
+      value = TRUE
+    ),
+    moransi = grep(
+      pattern = 'MoransI',
+      x = colnames(x = object[[]]),
+      value = TRUE
+    ),
+    abort(message = paste("Unknown method:", sQuote(x = method)))
+  )
+
+  tryCatch(
+    expr = svf.info <- object[[vars]],
+    error = function(e) {
+      stop(
+        "Unable to find spatially variable feature information for method '",
+        method,
+        "'",
+        call. = FALSE
+      )
+    }
+  )
+
+  colnames(x = svf.info) <- vars
+  if (status) {
+    svf.info$variable <- object[[paste0(method, '.spatially.variable')]]
+    svf.info$rank <- object[[paste0(method, '.spatially.variable.rank')]]
+  }
+  return(svf.info)
+}
+
+#' @rdname SpatiallyVariableFeatures-StdAssay
+#' @method SpatiallyVariableFeatures StdAssay
+#' @export
+#'
+SpatiallyVariableFeatures.StdAssay <- function(
+  object,
+  method = "moransi",
+  decreasing = TRUE,
+  selection.method = deprecated(),
+  ...
+) {
+  CheckDots(...)
+  if (is_present(arg = selection.method)) {
+    .Deprecate(
+      when = '5.0.0',
+      what = 'SpatiallyVariableFeatures(selection.method = )',
+      with = 'SpatiallyVariableFeatures(method = )'
+    )
+    method <- selection.method
+  }
+  vf <- SVFInfo(object = object, method = method, status = TRUE)
+  vf <- vf[rownames(x = vf)[which(!is.na(x = vf[, "variable"]))], ]
+  if (!is.null(x = decreasing)) {
+    vf <- vf[order(x = vf[, "rank"][, 1], decreasing = !decreasing), ]
+  }
+  return(rownames(x = vf))
+}
+
+#' @rdname SpatiallyVariableFeatures
+#' @method SpatiallyVariableFeatures Assay5
+#' @export
+#'
+SpatiallyVariableFeatures.Assay5 <- SpatiallyVariableFeatures.StdAssay
+
+#' @rdname VariableFeatures
+#' @method SVFInfo Assay5
+#' @export
+#'
+SVFInfo.Assay5 <- SVFInfo.StdAssay
+
 #' @method WhichCells StdAssay
 #' @export
 #'