From f41142b2ec009462b45302e2919e62a3d8849033 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Wed, 16 Oct 2024 09:46:42 -0400
Subject: [PATCH] temp

---
 R/clustering.R       | 30 +++++++++++++++++-------------
 man/labelTransfer.Rd |  9 +++++----
 2 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/R/clustering.R b/R/clustering.R
index f57dd4f84..7ca8141e8 100644
--- a/R/clustering.R
+++ b/R/clustering.R
@@ -3321,19 +3321,23 @@ setGeneric("labelTransfer",
 
 #' @rdname labelTransfer
 #' @export
-setMethod("labelTransfer", signature(x = "giotto", y = "giotto"), function(x, y,
-    spat_unit = NULL,
-    feat_type = NULL,
-    labels,
-    k = 10,
-    name = paste0("trnsfr_", labels),
-    prob = TRUE,
-    reduction = "cells",
-    reduction_method = "pca",
-    reduction_name = "pca",
-    dimensions_to_use = 1:10,
-    return_gobject = TRUE,
-    ...) {
+setMethod("labelTransfer", signature(x = "giotto", y = "giotto"), function(
+        x, y,
+        spat_unit = NULL,
+        feat_type = NULL,
+        labels,
+        k = 10,
+        name = paste0("trnsfr_", labels),
+        prob = TRUE,
+        co_filter_params = list(),
+        co_norm_params = list(),
+
+        reduction_name = NULL,
+        reduction_method = NULL,
+        dimensions_to_use = NULL,
+        return_gobject = TRUE,
+        ...
+) {
     # NSE vars
     temp_name <- cell_ID <- temp_name_prob <- NULL
 
diff --git a/man/labelTransfer.Rd b/man/labelTransfer.Rd
index dbf876a0b..230768609 100644
--- a/man/labelTransfer.Rd
+++ b/man/labelTransfer.Rd
@@ -16,10 +16,11 @@ voting}
   k = 10,
   name = paste0("trnsfr_", labels),
   prob = TRUE,
-  reduction = "cells",
-  reduction_method = "pca",
-  reduction_name = "pca",
-  dimensions_to_use = 1:10,
+  co_filter_params = list(),
+  co_norm_params = list(),
+  reduction_name = NULL,
+  reduction_method = NULL,
+  dimensions_to_use = NULL,
   return_gobject = TRUE,
   ...
 )