diff --git a/R/NN_network.R b/R/NN_network.R
index 45fe8eef..e41c0546 100644
--- a/R/NN_network.R
+++ b/R/NN_network.R
@@ -805,7 +805,7 @@ createNearestNetwork <- function(gobject,
         nn_names <- names(gobject@nn_network[[spat_unit]][[type]])
 
         if (name %in% nn_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+            wrap_msg(name, " has already been used, will be overwritten")
         }
 
         nnObj <- create_nn_net_obj(
@@ -915,10 +915,7 @@ addNetworkLayout <- function(
     if (return_gobject == TRUE) {
         nn_names <- names(gobject@nn_network[[spat_unit]][[nn_network_to_use]])
         if (layout_name %in% nn_names) {
-            cat(
-                "\n ", layout_name,
-                " has already been used, will be overwritten \n"
-            )
+            wrap_msg(layout_name," has already been used, will be overwritten")
         }
 
         gobject@nn_network[[spat_unit]][[
diff --git a/R/auxilliary.R b/R/auxilliary.R
index 6102105d..09a6f6b7 100644
--- a/R/auxilliary.R
+++ b/R/auxilliary.R
@@ -197,14 +197,11 @@ annotateGiotto <- function(
     no_matching_annotations <- uniq_names[!uniq_names %in% uniq_clusters]
 
     if (length(missing_annotations) > 0) {
-        cat(
-            "Not all clusters have an accompanying annotation in the
-            annotation_vector: \n",
-            "These names are missing: ", as.character(missing_annotations),
-            "\n",
-            "These annotations have no match: ",
-            as.character(no_matching_annotations), "\n"
-        )
+      wrap_msg("Not all clusters have an accompanying annotation in the
+          annotation_vector: \n", "These names are missing: ", 
+          as.character(missing_annotations), "\n",
+          "These annotations have no match: ", 
+          as.character(no_matching_annotations))
         stop("Annotation interrupted \n")
     }
 
@@ -1186,14 +1183,15 @@ calculateMetaTableCells <- function(
 
     if (!all(value_cols %in% cell_metadata_cols)) {
         missing_value_cols <- value_cols[!value_cols %in% cell_metadata_cols]
-        cat("These value columns were not found: ", missing_value_cols)
+        wrap_msg("These value columns were not found: ", missing_value_cols)
     }
     value_cols <- value_cols[value_cols %in% cell_metadata_cols]
 
     if (!all(metadata_cols %in% cell_metadata_cols)) {
         missing_metadata_cols <- metadata_cols[!metadata_cols %in%
             cell_metadata_cols]
-        cat("These metadata columns were not found: ", missing_metadata_cols)
+        wrap_msg("These metadata columns were not found: ", 
+                missing_metadata_cols)
     }
     metadata_cols <- metadata_cols[metadata_cols %in% cell_metadata_cols]
 
@@ -1340,7 +1338,7 @@ createMetafeats <- function(
         )
 
         if (name %in% spenr_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+          wrap_msg(name, " has already been used, will be overwritten")
         }
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
diff --git a/R/combine_metadata.R b/R/combine_metadata.R
index 9d5ba472..fd890ff1 100644
--- a/R/combine_metadata.R
+++ b/R/combine_metadata.R
@@ -703,7 +703,7 @@ calculateSpatCellMetadataProportions <- function(
 
 
         if (name %in% spenr_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+            wrap_msg(name, " has already been used, will be overwritten")
         }
 
         ## update parameters used ##
diff --git a/R/create.R b/R/create.R
index 62e712a4..3cd3e412 100644
--- a/R/create.R
+++ b/R/create.R
@@ -761,7 +761,7 @@ createGiottoObjectSubcellular <- function(gpolygons = NULL,
         polygon_dfr_list_params <- list(calc_centroids = FALSE)
     }
 
-    if (verbose) cat("1. Start extracting polygon information \n")
+    if (verbose) wrap_msg("1. Start extracting polygon information")
 
     polygon_res <- .extract_polygon_list(
         polygonlist = gpolygons,
@@ -770,18 +770,16 @@ createGiottoObjectSubcellular <- function(gpolygons = NULL,
     )
     gobject@spatial_info <- polygon_res
 
-    if (verbose) cat("2. Finished extracting polygon information \n")
+    if (verbose) wrap_msg("2. Finished extracting polygon information")
 
 
-    if (verbose) cat("3. Add centroid / spatial locations if available \n")
+    if (verbose) wrap_msg("3. Add centroid / spatial locations if available")
     for (polygon_info in list_spatial_info_names(gobject)) {
         centroidsDT <- gobject@spatial_info[[polygon_info]]@spatVectorCentroids
         if (!is.null(centroidsDT)) {
             if (verbose) {
-                cat(
-                    " - Add centroid / spatial locations for ",
-                    polygon_info, " \n"
-                )
+                wrap_msg(" - Add centroid / spatial locations for ",
+                    polygon_info)
             }
 
             centroidsDT <- .spatvector_to_dt(centroidsDT)
@@ -801,7 +799,7 @@ createGiottoObjectSubcellular <- function(gpolygons = NULL,
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
         }
     }
-    if (verbose) cat("3. Finish adding centroid / spatial locations \n")
+    if (verbose) wrap_msg("3. Finish adding centroid / spatial locations")
 
     ## cell ID ##
     ## ------- ##
@@ -818,13 +816,13 @@ createGiottoObjectSubcellular <- function(gpolygons = NULL,
 
 
     if (!is.null(gpoints)) {
-        if (verbose) cat("3. Start extracting spatial feature information \n")
+        if (verbose) wrap_msg("3. Start extracting spatial feature information")
 
         points_res <- .extract_points_list(pointslist = gpoints)
         gobject@feat_info <- points_res
 
         if (verbose) {
-            cat("4. Finished extracting spatial feature information \n")
+            wrap_msg("4. Finished extracting spatial feature information")
         }
 
         ## expression features ##
@@ -1160,7 +1158,7 @@ createGiottoObjectSubcellular <- function(gpolygons = NULL,
     ## largeImages ##
     # expect a list of giotto largeImages or file paths to such images
     if (!is.null(largeImages)) {
-        if (verbose) cat("3. Start loading large images \n")
+        if (verbose) wrap_msg("3. Start loading large images")
 
 
 
@@ -1214,7 +1212,7 @@ createGiottoObjectSubcellular <- function(gpolygons = NULL,
             }
         }
 
-        if (verbose) cat("4. Finished loading large images \n")
+        if (verbose) wrap_msg("4. Finished loading large images")
     }
 
     return(gobject)
@@ -3004,8 +3002,8 @@ createGiottoImage <- function(
             } else if (transf == "flip_y_axis") {
                 mg_object <- magick::image_flop(mg_object)
             } else {
-                cat(transf, " is not a supported transformation, see
-                    details \n")
+                wrap_msg(transf, " is not a supported transformation, see
+                    details")
             }
         }
     }
@@ -3015,11 +3013,8 @@ createGiottoImage <- function(
     ## 2. spatial minmax and adjustments -- manual OR by image dimensions (auto)
     if (verbose == TRUE) {
         if (do_manual_adj == TRUE) {
-            cat(
-                "do_manual_adj == TRUE \n",
-                "Boundaries will be adjusted by given
-                                    values.\n"
-            )
+            wrap_msg("do_manual_adj == TRUE \n",
+                    "Boundaries will be adjusted by given values.")
         }
     }
     # If spatlocs or gobject supplied, minmax values will always be generated
@@ -3252,7 +3247,7 @@ createGiottoLargeImage <- function(
     if (use_rast_ext == TRUE) {
         extent <- terra::ext(raster_object)
         if (verbose == TRUE) {
-            cat("use_rast_ext == TRUE, extent from input raster_object will
+            wrap_msg("use_rast_ext == TRUE, extent from input raster_object will
                 be used.")
         }
     }
@@ -3341,7 +3336,8 @@ createGiottoLargeImage <- function(
 
     if (nrow(sample_values) == 0) {
         if (verbose == TRUE) {
-            cat("No values discovered when sampling for image characteristics")
+            wrap_msg("No values discovered when sampling for image 
+                    characteristics")
         }
     } else {
         # find estimated intensity range
diff --git a/R/data_input.R b/R/data_input.R
index 71cb7d80..e3dc33eb 100644
--- a/R/data_input.R
+++ b/R/data_input.R
@@ -2201,7 +2201,7 @@ readPolygonData <- function(
                 ),
                 polygon_mask_list_params
             )
-            if (isTRUE(verbose)) print(parameters)
+            if (isTRUE(verbose)) wrap_msg(parameters)
 
             poly_results <- do.call(
                 what = "createGiottoPolygonsFromMask",
@@ -2216,7 +2216,7 @@ readPolygonData <- function(
                 ),
                 polygon_dfr_list_params
             )
-            if (isTRUE(verbose)) print(parameters)
+            if (isTRUE(verbose)) wrap_msg(parameters)
 
             poly_results <- do.call(
                 what = "createGiottoPolygonsFromDfr",
diff --git a/R/giotto_structures.R b/R/giotto_structures.R
index ffd7f827..52ba9889 100644
--- a/R/giotto_structures.R
+++ b/R/giotto_structures.R
@@ -347,7 +347,7 @@ smoothGiottoPolygons <- function(
         # adjust k to maximum value
         max_k <- nrow(polygMat)
         if (k >= max_k) {
-            cat("k will be set to ", max_k)
+            wrap_msg("k will be set to ", max_k)
             k <- max_k
         }
 
@@ -578,7 +578,7 @@ createSpatialFeaturesKNNnetwork_dbscan <- function(
     }
 
     ## 2. get spatial feature info and convert to matrix
-    if (verbose == TRUE) cat("Convert feature spatial info to matrix \n")
+    if (verbose == TRUE) wrap_msg("Convert feature spatial info to matrix")
     featDT <- .spatvector_to_dt(gobject@feat_info[[feat_type]]@spatVector)
     spatial_locations_matrix <- as.matrix(
         featDT[, c("x", "y", NULL), with = FALSE]
@@ -593,7 +593,7 @@ createSpatialFeaturesKNNnetwork_dbscan <- function(
     )
 
     ## 3. create kNN network
-    if (verbose == TRUE) cat("Create kNN network with dbscan \n")
+    if (verbose == TRUE) wrap_msg("Create kNN network with dbscan")
     knn_spatial <- dbscan::kNN(
         x = spatial_locations_matrix,
         k = k,
@@ -609,7 +609,7 @@ createSpatialFeaturesKNNnetwork_dbscan <- function(
 
     ## 3. keep minimum and filter
     if (verbose == TRUE) {
-        cat("Filter output for distance and minimum neighbours \n")
+        wrap_msg("Filter output for distance and minimum neighbours")
     }
     knn_sptial.norm[, rank := seq_len(.N), by = "from"]
 
@@ -632,7 +632,7 @@ createSpatialFeaturesKNNnetwork_dbscan <- function(
 
     ## 3. add feature information and sort
     if (add_feat_ids == TRUE) {
-        if (verbose == TRUE) cat("Add feat IDs and sort output \n")
+        if (verbose == TRUE) wrap_msg("Add feat IDs and sort output")
 
         featDT_vec <- featDT$feat_ID
         names(featDT_vec) <- featDT$feat_ID_uniq
@@ -731,7 +731,7 @@ createSpatialFeaturesKNNnetwork <- function(
         network_names <- names(gobject@feat_info[[feat_type]]@networks)
 
         if (name %in% network_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+            wrap_msg(name, " has already been used, will be overwritten")
         }
 
         gobject@feat_info[[feat_type]]@networks[[name]] <- knn_feat_network_obj
diff --git a/R/images.R b/R/images.R
index 9aaf6486..98c31de8 100644
--- a/R/images.R
+++ b/R/images.R
@@ -61,8 +61,8 @@ estimateImageBg <- function(mg_object, top_color_range = seq_len(50)) {
         col = names(sort_table[top_color_range])
     )
 
-    cat("Most abundant pixel colors: \n")
-    print(sort_table[top_color_range])
+    wrap_msg("Most abundant pixel colors:")
+    wrap_msg(sort_table[top_color_range])
 }
 
 
@@ -312,7 +312,7 @@ addGiottoImageMG <- function(
             )[1, ]
         } else {
             spat_loc_name <- NULL
-            cat("No spatial locations have been found \n")
+            wrap_msg("No spatial locations have been found")
         }
     }
 
@@ -324,8 +324,6 @@ addGiottoImageMG <- function(
 
         if ((length(scale_factor) == length(images)) ||
             length(scale_factor) == 1) {
-            # cat('scale_factor(s) external to giottoImage have been given and
-            # will be used')
             ext_scale_factor <- TRUE
         } else {
             stop("if scale_factor is given, it must be a numeric with either
@@ -352,8 +350,7 @@ addGiottoImageMG <- function(
             all_im_names <- names(gobject@images)
 
             if (im_name %in% all_im_names) {
-                cat("\n ", im_name, " has already been used, will be
-                    overwritten \n")
+                wrap_msg(im_name, " has already been used, will be overwritten")
             }
 
             # 3. Update boundaries if not already done during
@@ -491,7 +488,7 @@ updateGiottoImageMG <- function(
                 OR giottoImage argument(s) \n")
         }
         if (verbose == TRUE) {
-            cat("gobject argument not given \n return_gobject set to FALSE \n")
+            wrap_msg("gobject argument not given, return_gobject set to FALSE")
         }
         return_gobject <- FALSE
     }
@@ -505,8 +502,8 @@ updateGiottoImageMG <- function(
             stop("giottoImage argument only accepts giottoImage objects \n")
         }
         if (verbose == TRUE && !is.null(gobject)) {
-            cat("giottoImage argument is given and will take priority \n
-                return_gobject set to FALSE \n")
+            wrap_msg("giottoImage argument is given and will take priority \n
+                return_gobject set to FALSE")
         }
         return_gobject <- FALSE
     }
@@ -1168,17 +1165,12 @@ stitchGiottoLargeImage <- function(
     if (file.exists(filename)) {
         if (verbose == TRUE) {
             if (overwrite == TRUE) {
-                cat(
-                    "File at", filename,
-                    "exists.\n (overwrite == TRUE) Image will be overwritten"
-                )
+                wrap_msg("File at", filename,
+                    "exists.\n (overwrite == TRUE) Image will be overwritten")
             }
             if (overwrite == FALSE) {
-                cat(
-                    "File at", filename,
-                    "exists.\n (overwrite == FALSE) Image will not be
-                    overwritten"
-                )
+                wrap_msg("File at", filename, "exists.\n 
+                    (overwrite == FALSE) Image will not be overwritten")
             }
         }
     }
@@ -1255,8 +1247,8 @@ stitchGiottoLargeImage <- function(
     # integer extents)
     if (round_positions == TRUE) {
         if (verbose == TRUE) {
-            cat("round_positions == TRUE \n Image spatial positions will be
-                rounded to integers. \n")
+            wrap_msg("round_positions == TRUE \n Image spatial positions will be
+                rounded to integers.")
         }
         for (rast_i in seq_len(length(raster_list))) {
             terra::ext(raster_list[[rast_i]]) <- round(
@@ -1564,8 +1556,7 @@ convertGiottoLargeImageToMG <- function(
     if (return_gobject == TRUE) {
         if (verbose == TRUE) {
             if (mg_name %in% names(gobject@images)) {
-                cat("\n ", mg_name, " has already been used, will be
-                    overwritten \n")
+                wrap_msg(mg_name, " has already been used, will be overwritten")
             }
         }
         gobject@images[[mg_name]] <- g_image
@@ -1697,7 +1688,7 @@ convertGiottoLargeImageToMG <- function(
         }
     } else if (!is.null(quick_INTS_maxval)) {
         if (isTRUE(verbose)) {
-            cat("Selecting compatible datatype for given maximum value \n")
+            wrap_msg("Selecting compatible datatype for given maximum value")
         }
         bitDepth <- .bitdepth(quick_INTS_maxval)
     }
@@ -1805,11 +1796,11 @@ writeGiottoLargeImage <- function(
         if (file.exists(filename)) {
             if (verbose == TRUE) {
                 if (overwrite == TRUE) {
-                    cat("File at", filename, "exists.\n (overwrite == TRUE)
+                    wrap_msg("File at", filename, "exists.\n (overwrite == TRUE)
                         Image will be overwritten")
                 }
                 if (overwrite == FALSE) {
-                    cat("File at", filename, "exists.\n (overwrite == FALSE)
+                    wrap_msg("File at", filename, "exists.\n (overwrite == FALSE)
                         Image will not be overwritten")
                 }
             }
@@ -1860,7 +1851,7 @@ writeGiottoLargeImage <- function(
 
 
     ## 3. Write to disk
-    if (verbose == TRUE) cat(paste0("Writing image to disk as ", dataType))
+    if (verbose == TRUE) wrap_msg("Writing image to disk as ", dataType)
     terra::writeRaster(
         x = raster_object,
         filename = filename,
@@ -1919,7 +1910,7 @@ updateGiottoLargeImage <- function(
                 largeImage_name OR giottoLargeImage argument(s) \n")
         }
         if (verbose == TRUE) {
-            cat("gobject argument not given \n return_gobject set to FALSE \n")
+            wrap_msg("gobject argument not given, return_gobject set to FALSE")
         }
         return_gobject <- FALSE
     }
@@ -1934,8 +1925,8 @@ updateGiottoLargeImage <- function(
                 objects \n")
         }
         if (verbose == TRUE && !is.null(gobject)) {
-            cat("giottoLargeImage argument is given and will take priority
-                \n return_gobject set to FALSE \n")
+            wrap_msg("giottoLargeImage argument is given and will take priority
+                \n return_gobject set to FALSE")
         }
         return_gobject <- FALSE
     }
@@ -2097,8 +2088,6 @@ addGiottoLargeImage <- function(
 
         if ((length(scale_factor) == length(largeImages)) ||
             length(scale_factor) == 1) {
-            # cat('scale_factor(s) external to giottoImage have been given and
-            # will be used')
             ext_scale_factor <- TRUE
         } else {
             stop("if scale_factor is given, it must be a numeric with either
@@ -2125,10 +2114,8 @@ addGiottoLargeImage <- function(
             all_im_names <- names(gobject@largeImages)
 
             if (im_name %in% all_im_names) {
-                cat(
-                    "\n ", im_name,
-                    " has already been used, will be overwritten \n"
-                )
+                wrap_msg("\n ", im_name,
+                    " has already been used, will be overwritten")
             }
 
             # Deep copy the raster_object
@@ -2314,7 +2301,6 @@ plotGiottoImage <- function(
     }
 
     # Select plotting function
-    # cat('Plotting ', image_type, ': "', image_name, '" ... \n', sep = '')
 
     if (image_type == "image") {
         .plot_giottoimage_mg(giottoImage = img_obj)
@@ -2691,7 +2677,7 @@ reconnectGiottoImage <- function(
 
     #### Auto Workflow
     if (auto_reconnect == TRUE) {
-        if (verbose == TRUE) cat("Attempting automatic reconnection...\n\n")
+        if (verbose == TRUE) wrap_msg("Attempting automatic reconnection...")
 
         # Find image_types to reconnect
         image_type_list <- unique(availableImgs$img_type)
@@ -2724,36 +2710,32 @@ reconnectGiottoImage <- function(
             # print discovered images and paths
             # additionally, set path to NULL if file.exists() == FALSE
             if (verbose == TRUE) {
-                cat(image_type, "(s) discovered...\n", sep = "")
+                wrap_msg(image_type, "(s) discovered...", sep = "")
             }
 
             for (image_i in seq_len(length(img_path[[image_type]]))) {
                 if (!is.null(img_path[[image_type]][[image_i]])) {
                     if (verbose == TRUE) {
-                        cat(
-                            "-->", name_list[[image_type]][[image_i]],
-                            ": filepath found"
-                        )
+                        wrap_msg("-->", name_list[[image_type]][[image_i]],
+                            ": filepath found")
                     }
                     if (!file.exists(img_path[[image_type]][[image_i]])) {
-                        if (verbose == TRUE) cat("but file is missing\n")
+                        if (verbose == TRUE) wrap_msg("but file is missing")
                         img_path[[image_type]][[image_i]] <- NULL
-                    } else if (verbose == TRUE) cat("\n")
+                    } else if (verbose == TRUE) wrap_msg("\n")
                 } else if (verbose == TRUE) {
-                    cat(
-                        "-->", name_list[[image_type]][[image_i]],
-                        ": filepath NOT found\n"
-                    )
+                    wrap_msg("-->", name_list[[image_type]][[image_i]],
+                        ": filepath NOT found")
                 }
             }
-            if (verbose == TRUE) cat("\n")
+            if (verbose == TRUE) wrap_msg("\n")
         } # image_type end loop
 
 
 
         #### Manual Workflow
     } else {
-        if (verbose == TRUE) cat("Reconnecting with manual input...\n\n")
+        if (verbose == TRUE) wrap_msg("Reconnecting with manual input...")
 
         # Check params
         # filepath list(s) must be given as input
@@ -2845,20 +2827,17 @@ reconnectGiottoImage <- function(
                 img_path[[image_type]]
             )) {
                 if (verbose == TRUE) {
-                    cat(image_type, ": no filepaths found. Skipping. \n")
+                    wrap_msg(image_type, ": no filepaths found. Skipping.")
                 }
                 next
             }
 
             if (verbose == TRUE) {
-                cat("\n Skipping ", image_type,
-                    "s with missing filepaths: \n",
-                    sep = ""
-                )
-                for (image_NULL_i in seq_len(sum(image_path_NULL[[image_type]]))) {
-                    cat(name_list[[image_type]][[which(
-                        image_path_NULL[[image_type]]
-                    )[[image_NULL_i]]]], "\n")
+                wrap_msg("Skipping ", image_type, "s with missing filepaths:")
+                for (image_NULL_i in 
+                    seq_len(sum(image_path_NULL[[image_type]]))) {
+                    wrap_msg(name_list[[image_type]][[which(
+                        image_path_NULL[[image_type]])[[image_NULL_i]]]])
                 }
             }
 
@@ -2899,7 +2878,7 @@ reconnectGiottoImage <- function(
             )
         }
 
-        if (verbose == TRUE) cat("done \n")
+        if (verbose == TRUE) wrap_msg("done")
     } # image_type end loop
     return(gobject)
 }
diff --git a/R/interoperability.R b/R/interoperability.R
index f3b679a5..497966a4 100644
--- a/R/interoperability.R
+++ b/R/interoperability.R
@@ -128,8 +128,8 @@ check_py_for_scanpy <- function() {
             \n
             ", errWidth = TRUE))
     } else if (module_test == FALSE && genv_in_use) {
-        cat("Python module scanpy is required for conversion.
-          Installing scanpy now in the Giotto Miniconda Environment.\n")
+        wrap_msg("Python module scanpy is required for conversion.
+          Installing scanpy now in the Giotto Miniconda Environment.")
 
         conda_path <- reticulate::miniconda_path()
         py_ver <- reticulate::py_config()$version_string
@@ -147,8 +147,8 @@ check_py_for_scanpy <- function() {
             python_version = py_ver
         )
     } else {
-        cat("Required Python module scanpy has been previously installed.
-            Proceeding with conversion.\n")
+        wrap_msg("Required Python module scanpy has been previously installed.
+            Proceeding with conversion.")
     }
 }
 
@@ -631,10 +631,10 @@ giottoToAnnData <- function(
     } else if (!dir.exists(save_directory)) {
         warning(wrap_msg("Provided save directory not found. Creating save
                         directory at location:"))
-        cat(save_directory)
+        wrap_msg(save_directory)
         dir.create(save_directory, recursive = TRUE)
         if (dir.exists(save_directory)) {
-            cat("Created directory", save_directory)
+            wrap_msg("Created directory", save_directory)
         } else {
             stop(wrap_msg("Unable to create directory. Please change the
                         provided path and try again."))
diff --git a/R/join.R b/R/join.R
index b118620b..f99ab36c 100644
--- a/R/join.R
+++ b/R/join.R
@@ -437,14 +437,13 @@ joinGiottoObjects <- function(
                     }
 
                     if (verbose) {
-                        cat(
-                            "Image: for ", imname, " add_to_x = ",
-                            add_to_x, "\n"
-                        )
+                        wrap_msg("Image: for ", imname, " add_to_x = ",
+                            add_to_x)
                     }
 
                     gobj@images[[imname]]@minmax[c("xmax_sloc", "xmin_sloc")] <-
-                        gobj@images[[imname]]@minmax[c("xmax_sloc", "xmin_sloc")] + add_to_x
+                        gobj@images[[imname]]@minmax[c(
+                            "xmax_sloc", "xmin_sloc")] + add_to_x
                     xshift_list[[gobj_i]] <- add_to_x
 
 
@@ -454,16 +453,14 @@ joinGiottoObjects <- function(
                         add_to_y <- y_shift_i + (y_padding * (gobj_i - 1))
 
                         if (verbose) {
-                            cat(
-                                "Image: for ", imname, " add_to_y = ",
-                                add_to_y, "\n"
-                            )
+                            wrap_msg("Image: for ", imname, " add_to_y = ",
+                                add_to_y)
                         }
 
-                        gobj@images[[imname]]@minmax[c("ymax_sloc", "ymin_sloc")] <- gobj@images[[imname]]@minmax[c(
-                            "ymax_sloc",
-                            "ymin_sloc"
-                        )] + add_to_y
+                        gobj@images[[imname]]@minmax[
+                            c("ymax_sloc", "ymin_sloc")] <- gobj@images[[
+                                imname]]@minmax[c("ymax_sloc","ymin_sloc")] + 
+                            add_to_y
                         yshift_list[[gobj_i]] <- add_to_y
                     }
                 }
@@ -516,10 +513,8 @@ joinGiottoObjects <- function(
 
 
                     if (verbose) {
-                        cat(
-                            "largeImage: for ", imname, " add_to_x = ",
-                            add_to_x, "\n"
-                        )
+                        wrap_msg("largeImage: for ", imname, " add_to_x = ",
+                            add_to_x)
                     }
 
 
@@ -542,10 +537,8 @@ joinGiottoObjects <- function(
 
 
                         if (verbose) {
-                            cat(
-                                "largeImage: for ", imname, " add_to_y = ",
-                                add_to_y, "\n"
-                            )
+                            wrap_msg("largeImage: for ", imname, " add_to_y = ",
+                                add_to_y)
                         }
 
 
@@ -611,10 +604,8 @@ joinGiottoObjects <- function(
                     }
 
                     if (verbose) {
-                        cat(
-                            "Spatial locations: for ", locs_i,
-                            " add_to_x = ", add_to_x, "\n"
-                        )
+                        wrap_msg("Spatial locations: for ", locs_i,
+                            " add_to_x = ", add_to_x)
                     }
 
 
@@ -630,10 +621,8 @@ joinGiottoObjects <- function(
                     add_to_y <- y_shift_i + (y_padding * (gobj_i - 1))
 
                     if (verbose) {
-                        cat(
-                            "Spatial locations: for ", locs_i,
-                            " add_to_y = ", add_to_y, "\n"
-                        )
+                        wrap_msg("Spatial locations: for ", locs_i,
+                            " add_to_y = ", add_to_y)
                     }
 
                     myspatlocs[, sdimy := sdimy + add_to_y]
@@ -721,16 +710,12 @@ joinGiottoObjects <- function(
                 }
 
                 if (verbose) {
-                    cat(
-                        "Spatial info: for ", spat_info, " add_to_x = ",
-                        add_to_x, "\n"
-                    )
+                    wrap_msg("Spatial info: for ", spat_info, " add_to_x = ",
+                        add_to_x)
                 }
                 if (verbose) {
-                    cat(
-                        "Spatial info: for ", spat_info, " add_to_y = ",
-                        add_to_y, "\n"
-                    )
+                    wrap_msg("Spatial info: for ", spat_info, " add_to_y = ",
+                        add_to_y)
                 }
 
                 gobj@spatial_info[[spat_info]]@spatVector <- terra::shift(
@@ -786,16 +771,12 @@ joinGiottoObjects <- function(
                 }
 
                 if (verbose) {
-                    cat(
-                        "Feature info: for ", feat_info, " add_to_x = ",
-                        add_to_x, "\n"
-                    )
+                    wrap_msg("Feature info: for ", feat_info, " add_to_x = ",
+                        add_to_x)
                 }
                 if (verbose) {
-                    cat(
-                        "Feature info: for ", feat_info, " add_to_y = ",
-                        add_to_y, "\n"
-                    )
+                    wrap_msg("Feature info: for ", feat_info, " add_to_y = ",
+                        add_to_y)
                 }
 
                 gobj@feat_info[[feat_info]]@spatVector <- terra::shift(
@@ -1045,7 +1026,7 @@ joinGiottoObjects <- function(
 
     if (isTRUE(verbose)) {
         wrap_msg("available_spat_info: \n")
-        print(available_spat_info)
+        wrap_msg(available_spat_info)
     }
 
     for (spat_info in available_spat_info) {
diff --git a/R/methods-initialize.R b/R/methods-initialize.R
index b3cf385c..780f2d50 100644
--- a/R/methods-initialize.R
+++ b/R/methods-initialize.R
@@ -207,7 +207,7 @@ setMethod("initialize", signature("giotto"), function(.Object, ...) {
             exp_list_names <- lapply(exp_list, spatIDs)
             list_match <- sapply(exp_list_names, setequal, exp_list_names[[1L]])
             if (!all(list_match)) {
-                print(list_match)
+                wrap_msg(list_match)
                 warning(wrap_txt(
                     "spat_unit:", unique_expr_sets$spat_unit[[set_i]], "/",
                     "feat_type:", unique_expr_sets$feat_type[[set_i]],
diff --git a/R/save_load.R b/R/save_load.R
index 6c29059e..57c4d366 100644
--- a/R/save_load.R
+++ b/R/save_load.R
@@ -374,7 +374,7 @@ loadGiotto <- function(
         )
 
         for (feat_i in seq_len(length(feat_names))) {
-            if (verbose) print(feat_paths[feat_i])
+            if (verbose) wrap_msg(feat_paths[feat_i])
             spatVector <- terra::vect(x = feat_paths[feat_i])
 
             # read in original column names and assign to spatVector
@@ -385,7 +385,7 @@ loadGiotto <- function(
             names(spatVector) <- spatVector_names
 
             feat_name <- feat_names[feat_i]
-            if (verbose) print(feat_name)
+            if (verbose) wrap_msg(feat_name)
             gobject@feat_info[[feat_name]]@spatVector <- spatVector
         }
     }
@@ -410,8 +410,8 @@ loadGiotto <- function(
     if (length(spat_files) != 0) {
         ## 3.1. shapes
         if (isTRUE(verbose)) {
-            wrap_msg("\n3.1 read Giotto spatial shape information \n")
-            print(spat_files)
+            wrap_msg("3.1 read Giotto spatial shape information")
+            wrap_msg(spat_files)
         }
 
         spat_names <- gsub(spat_files,
@@ -513,10 +513,10 @@ loadGiotto <- function(
         if (length(overlap_files) == 0) {
             if (verbose) {
                 wrap_msg("No overlaps were found, overlap loading will be
-                        skipped \n")
+                        skipped")
             }
         } else {
-            print(overlap_files)
+            wrap_msg(overlap_files)
 
             # find overlaps per spatVector
             for (sv_i in seq_along(overlap_search_term)) {
@@ -544,7 +544,7 @@ loadGiotto <- function(
                         input = overlap_paths_colnames[spat_i],
                         header = FALSE
                     )[["V1"]]
-                    if (verbose) print(spatVector_names)
+                    if (verbose) wrap_msg(spatVector_names)
                     names(spatVector) <- spatVector_names
 
                     feat_name <- gsub(overlap_filenames[spat_i],
diff --git a/R/slot_accessors.R b/R/slot_accessors.R
index d87b0cdf..ea6012ae 100644
--- a/R/slot_accessors.R
+++ b/R/slot_accessors.R
@@ -979,35 +979,6 @@ set_cell_metadata <- function(
     }
 
 
-    # old_meta = data.table::copy(
-    # gobject@cell_metadata[[spat_unit]][[feat_type]])
-    #
-    # new_cols = NULL
-    # if(!is.null(old_meta) && inherits(old_meta, "data.table")){
-    #   old_cols = colnames(old_meta)
-    #   new_cols = colnames(meta_dt)
-    #   cat("\nWarning: The following columns will be overwritten:",
-    #   old_cols, "\nThey will be replaced with:", new_cols,"\n")
-    #
-    #   old_meta[, (old_cols) := NULL]
-    #
-    # } else {
-    #   new_cols = colnames(meta_dt)
-    #   cat("\nWriting data within columns:", new_cols,
-    #   "\nto cell metadata\n")
-    # }
-
-    # suppressWarnings({
-    #   gobject <- removeCellAnnotation(gobject = gobject,
-    #                                   spat_unit = spat_unit,
-    #                                   feat_type = feat_type,
-    #                                   columns = old_cols,
-    #                                   return_gobject = TRUE)
-    #   gobject@cell_metadata[[spat_unit]][[feat_type]] = meta_dt
-    # })
-    # message("\nCell Metadata slot '",spat_unit, feat_type, "' set.\n")
-    #
-
     # 6. set and return gobject
     gobject@cell_metadata[[spat_unit]][[feat_type]] <- metadata
 
@@ -2317,11 +2288,9 @@ get_spatial_locations <- function(
             spat_loc_name <- names(
                 slot(gobject, "spatial_locs")[[spat_unit]]
             )[[1]]
-            # cat('No spatial locations have been selected, the first
-            # one -',spat_loc_name, '- will be used \n')
         } else {
             spat_loc_name <- NULL
-            cat("No spatial locations have been found \n")
+            wrap_msg("No spatial locations have been found")
             return(NULL)
         }
     }
@@ -5329,11 +5298,9 @@ get_spatial_enrichment <- function(
                 spat_unit = spat_unit,
                 feat_type = feat_type
             )[[1]]
-            # cat('No spatial locations have been selected, the first
-            # one -',spat_loc_name, '- will be used \n')
         } else {
             enrichm_name <- NULL
-            cat("No spatial enrichment results have been found \n")
+            wrap_msg("No spatial enrichment results have been found")
             return(NULL)
         }
     }
diff --git a/R/spatial_structures.R b/R/spatial_structures.R
index 271c2fe9..ada67646 100644
--- a/R/spatial_structures.R
+++ b/R/spatial_structures.R
@@ -824,7 +824,7 @@ spat_net_to_igraph <- function(spatialNetworkObj, attr = NULL) {
             spat_unit = spat_unit
         )
         if (name %in% spn_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+            wrap_msg(name, " has already been used, will be overwritten")
         }
         parameters_list <- slot(gobject, "parameters")
         number_of_rounds <- length(parameters_list)
@@ -997,10 +997,7 @@ spat_net_to_igraph <- function(spatialNetworkObj, attr = NULL) {
             spat_unit = "cell"
         )
         if (name %in% spn_names) {
-            cat(
-                "\n ", name,
-                " has already been used, will be overwritten \n"
-            )
+            wrap_msg(name, " has already been used, will be overwritten")
         }
         parameters_list <- gobject@parameters
         number_of_rounds <- length(parameters_list)
@@ -1508,7 +1505,7 @@ createSpatialKNNnetwork <- function(
         )
 
         if (name %in% spn_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+            wrap_msg(name, " has already been used, will be overwritten")
         }
         parameters_list <- slot(gobject, "parameters")
         number_of_rounds <- length(parameters_list)
@@ -2283,7 +2280,7 @@ createSpatialDefaultGrid <- function(
         )
 
         if (name %in% spg_names) {
-            cat("\n ", name, " has already been used, will be overwritten \n")
+            wrap_msg(name, " has already been used, will be overwritten")
         }
 
         # 2. create spatial grid object
@@ -2321,8 +2318,6 @@ createSpatialDefaultGrid <- function(
         # parent function name
         cl <- sys.call(-1)
 
-        # print('cl = ')
-        # print(cl)
 
         if (is.null(cl)) {
             gobject <- update_giotto_params(gobject, description = "_grid")
@@ -2602,11 +2597,8 @@ annotateSpatialGrid <- function(
         missing_annotation <- annotation_vector[!annotation_vector %in%
             possible_annotations]
         if (length(missing_annotation) > 0) {
-            cat(
-                "These annotations were not found back in the cell metadata
-                (pDataDT): \n",
-                missing_annotation, "\n"
-            )
+            wrap_msg("These annotations were not found back in the cell metadata
+                (pDataDT): \n", missing_annotation)
         }
 
         annotation_vector_found <- annotation_vector[annotation_vector %in%
diff --git a/R/stitch_coordinates.R b/R/stitch_coordinates.R
index 9d8cebd3..5ee4a496 100644
--- a/R/stitch_coordinates.R
+++ b/R/stitch_coordinates.R
@@ -112,13 +112,13 @@ stitchTileCoordinates <- function(
     Xcoord <- X.X <- XtileIndex <- Ycoord <- Y.Y <- YtileIndex <- NULL
 
     if (is.null(location_file$X.X)) {
-        print("X coordinates missing in input file.")
+        wrap_msg("X coordinates missing in input file.")
     } else if (is.null(location_file$Y.Y)) {
-        print("Y coordinates missing in input file.")
+        wrap_msg("Y coordinates missing in input file.")
     } else if (is.null(location_file$XtileIndex)) {
-        print("X tile index missing in input file.")
+        wrap_msg("X tile index missing in input file.")
     } else if (is.null(location_file$YtileIndex)) {
-        print("Y tile index missing in input file.")
+        wrap_msg("Y tile index missing in input file.")
     } else {
         copy_loc_file <- data.table::copy(location_file)
         copy_loc_file[, Xcoord := X.X + Xtilespan * (XtileIndex - 1)]
diff --git a/R/subset.R b/R/subset.R
index 77c71c0c..cd2a90ae 100644
--- a/R/subset.R
+++ b/R/subset.R
@@ -566,16 +566,14 @@
     res_list <- list()
     # iterate through all spatial info entries...
     for (spat_info in names(spatial_info)) {
-        if (verbose) cat("for ", spat_info, "\n")
+        if (verbose) wrap_msg("for ", spat_info)
         si <- spatial_info[[spat_info]]
 
         # if the spatial info is one selected in poly_info:
         if (spat_info %in% poly_info) {
             if (verbose) {
-                cat(
-                    "--> ", spat_info, " found back in polygon layer: ",
-                    poly_info, "\n"
-                )
+                wrap_msg("--> ", spat_info, " found back in polygon layer: ",
+                    poly_info)
             }
 
             # # whitelist check
@@ -583,14 +581,6 @@
             # # that no spatial locations
             # # or expression info was discovered for the selected
             # # spat_unit
-            # if (!is.null(poly_whitelist)) {
-            #   if (!objName(si) %in% poly_whitelist) {
-            #     warning(wrap_txt(
-            #       'poly', objName(si), 'not in spat_unit or provenance of
-            # .      aggregate spatial locations or expression'
-            #     ))
-            #   }
-            # }
 
             # check if cell_ids to keep and poly_ids of polygon have any overlap
             # warn if none
@@ -669,7 +659,7 @@
     res_list <- list()
     for (feat in names(feat_info)) {
         if (isTRUE(feat %in% feat_type)) {
-            if (verbose) cat("subset feature info:", feat)
+            if (verbose) wrap_msg("subset feature info:", feat)
 
             feat_subset <- .subset_giotto_points_object(
                 gpoints = feat_info[[feat]],
@@ -801,7 +791,7 @@
 
 
 
-    if (verbose) cat("completed 1: preparation \n")
+    if (verbose) wrap_msg("completed 1: preparation")
 
 
     ## FILTER ##
@@ -816,7 +806,7 @@
         feat_type_ssub = feat_type_ssub
     )
 
-    if (verbose) cat("completed 2: subset expression data \n")
+    if (verbose) wrap_msg("completed 2: subset expression data")
 
 
     # filter spatial locations
@@ -827,7 +817,7 @@
         spat_unit = spat_unit
     )
 
-    if (verbose) cat("completed 3: subset spatial locations \n")
+    if (verbose) wrap_msg("completed 3: subset spatial locations")
 
 
 
@@ -840,7 +830,7 @@
         cell_ids = cell_ids
     )
 
-    if (verbose) cat("completed 4: subset cell metadata \n")
+    if (verbose) wrap_msg("completed 4: subset cell metadata")
 
     # feature metadata
     gobject <- .subset_feature_metadata(
@@ -850,7 +840,7 @@
         feat_ids = feat_ids
     )
 
-    if (verbose) cat("completed 5: subset feature metadata \n")
+    if (verbose) wrap_msg("completed 5: subset feature metadata")
 
 
     ## spatial network & grid ##
@@ -862,7 +852,7 @@
     )
 
 
-    if (verbose) cat("completed 6: subset spatial network(s) \n")
+    if (verbose) wrap_msg("completed 6: subset spatial network(s)")
 
     # spatial grid
     # need to be recomputed
@@ -881,7 +871,7 @@
     )
     # likely also needs to be recomputed
 
-    if (verbose) cat("completed 7: subsetted dimension reductions \n")
+    if (verbose) wrap_msg("completed 7: subsetted dimension reductions")
 
 
     ## nn network ##
@@ -892,7 +882,7 @@
         cell_ids = cell_ids
     )
 
-    if (verbose) cat("completed 8: subsetted nearest network(s) \n")
+    if (verbose) wrap_msg("completed 8: subsetted nearest network(s)")
 
 
     ## spatial enrichment ##
@@ -903,7 +893,7 @@
         cell_ids = cell_ids
     )
 
-    if (verbose) cat("completed 9: subsetted spatial enrichment results \n")
+    if (verbose) wrap_msg("completed 9: subsetted spatial enrichment results")
 
     ## spatial info
     if (!is.null(gobject@spatial_info)) {
@@ -912,10 +902,6 @@
         # # aggregate spatial locations and expression information
         # #
         # # Should only be checked for cell_ids subsets
-        # poly_whitelist = poly_provenance_whitelist(
-        #   gobject = gobject,
-        #   spat_unit = spat_unit
-        # )
 
         for (select_poly_info in poly_info) {
             # For each entry entry in poly_info, subset using cell_ids.
@@ -937,7 +923,8 @@
             )
         }
 
-        if (verbose) cat("completed 10: subsetted spatial information data \n")
+        if (verbose) 
+            wrap_msg("completed 10: subsetted spatial information data")
     }
 
 
@@ -954,7 +941,7 @@
             verbose = verbose
         )
 
-        if (verbose) cat("completed 11: subsetted spatial feature data \n")
+        if (verbose) wrap_msg("completed 11: subsetted spatial feature data")
     }
 
 
@@ -1112,8 +1099,6 @@
                 gobject = gobject,
                 spat_unit = spat_unit
             )[[1]]
-            # cat('No spatial locations have been selected, the first
-            # one -',spat_loc_name, '- will be used \n')
 
             # if spatlocs missing, use alternate method with spatial_info
         } else if (!is.null(slot(gobject, "spatial_info"))) {
diff --git a/R/zzz.R b/R/zzz.R
index 6e112df4..6217d886 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -2,29 +2,6 @@
 
 
 .onAttach <- function(libname, pkgname) {
-    ## Giotto Utils ##
-    # utils_try = try(
-    #   library(GiottoUtils),
-    #   silent = TRUE
-    # )
-    #
-    # if(inherits(utils_try, 'try-error')) {
-    #   if (utils::menu(c("Yes", "No"),
-    #                   title = "GiottoUtils is required. Proceed with
-    #                   installation?") == "1") {
-    #     devtools::install_github('drieslab/GiottoUtils')
-    #
-    #   } else {
-    #     print("Cancelling installation")
-    #     stop('There is no package called GiottoUtils', call. = FALSE)
-    #   }
-    # }
-
-    # set GiottoClass options
-    # options("giotto.use_conda" = FALSE)
-
-    ## print version number ##
-
     check_ver <- getOption("giotto.check_version", TRUE)
     if (isTRUE(check_ver)) {
         GiottoUtils::check_github_suite_ver("GiottoClass")
diff --git a/man/crop.Rd b/man/crop.Rd
index 731a83fd..baa9080e 100644
--- a/man/crop.Rd
+++ b/man/crop.Rd
@@ -3,12 +3,15 @@
 \name{crop}
 \alias{crop}
 \alias{crop,giottoLargeImage-method}
+\alias{crop,spatLocsObj-method}
 \alias{crop,giottoPoints-method}
 \alias{crop,giottoPolygon-method}
 \title{Crop to a spatial subset}
 \usage{
 \S4method{crop}{giottoLargeImage}(x, y, ...)
 
+\S4method{crop}{spatLocsObj}(x, y, ...)
+
 \S4method{crop}{giottoPoints}(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)
 
 \S4method{crop}{giottoPolygon}(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)
@@ -40,15 +43,6 @@ the polygon that does fall within the selected crop region.
 Set \code{DT = FALSE} in order to use the default style of terra::crop behavior
 that also allows usage of additional params through ...
 }
-\section{Methods (by class)}{
-\itemize{
-\item \code{crop(giottoLargeImage)}: Crop a giottoLargeImage
-
-\item \code{crop(giottoPoints)}: Crop a giottoPoints
-
-\item \code{crop(giottoPolygon)}: Crop a giottoPoints
-
-}}
 \examples{
 g <- GiottoData::loadGiottoMini("visium")
 g_image <- getGiottoImage(g, image_type = "largeImage")