Merge pull request #187 from josschavezf/dev

replace cat and print with wrap_msg
drieslab · Apr 12, 2024 · cc3030e · cc3030e
2 parents e119ac1 + bb2cebf
commit cc3030e
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Showing 17 changed files with 149 additions and 283 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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