add verbose arguements to some functions

R/conversion.R

@@ -4,6 +4,7 @@
 
 #' @param type the spatial data type of Seurat object: "image" or "spatial"
 #' @param assay_name the assay name
+#' @param verbose verbose
 #' @param ... Additional parameter passed to \link{formVoltRon}
 #'
 #' @rdname as.VoltRon
@@ -12,7 +13,7 @@
 #' @importFrom stringr str_replace str_extract
 #' @export
 #'
-as.VoltRon.Seurat <- function(object, type = c("image", "spatial"), assay_name = NULL, ...){
+as.VoltRon.Seurat <- function(object, type = c("image", "spatial"), assay_name = NULL, verbose = TRUE, ...){
 
   # check Seurat package
   if(!requireNamespace('Seurat'))
@@ -40,7 +41,8 @@ as.VoltRon.Seurat <- function(object, type = c("image", "spatial"), assay_name =
     for(fn in fov_names){
 
       # message
-      message("Converting FOV: ", fn, " ...")
+      if(verbose)
+        message("Converting FOV: ", fn, " ...")
 
       # image object
       spatialobject <- spatialobjectlist[[fn]]
@@ -83,7 +85,8 @@ as.VoltRon.Seurat <- function(object, type = c("image", "spatial"), assay_name =
     }
 
     # merge object
-    message("Merging object ...")
+    if(verbose)
+      message("Merging object ...")
     vrobject <- merge(voltron_list[[1]], voltron_list[-1])
   } else{
     image <- NULL
@@ -745,6 +748,7 @@ as.Giotto <- function(object, assay = NULL, reg = FALSE){
 #' @param assay_type one of two types, 'cell' or 'spot' etc.
 #' @param assay_name the assay name of the voltron assays (e.g. Visium, Xenium etc.)
 #' @param image_id select image_id names if needed.
+#' @param verbose verbose
 #' @param ... Additional parameter passed to \link{formVoltRon}
 #'
 #' @rdname as.VoltRon
@@ -753,7 +757,7 @@ as.Giotto <- function(object, assay = NULL, reg = FALSE){
 #' @importFrom magick image_read
 #'
 #' @export
-as.VoltRon.SpatialExperiment <- function(object, assay_type = "cell", assay_name = NULL, image_id = NULL, ...){
+as.VoltRon.SpatialExperiment <- function(object, assay_type = "cell", assay_name = NULL, image_id = NULL, verbose = TRUE, ...){
 
   # check SpatialExperiment package
   if(!requireNamespace('SpatialExperiment'))
@@ -846,7 +850,8 @@ as.VoltRon.SpatialExperiment <- function(object, assay_type = "cell", assay_name
   }
 
   # merge object
-  message("Merging object ...")
+  if(verbose)
+    message("Merging object ...")
   if(length(voltron_list) > 1){
     vrobject <- merge(voltron_list[[1]], voltron_list[-1])
   } else {

R/objects.R

@@ -1052,14 +1052,15 @@ subset.VoltRon <- function(object, subset, samples = NULL, assays = NULL, spatia
 #' @param object_list a list of VoltRon objects
 #' @param samples a single sample name or multiple sample names of the same size as the given VoltRon objects
 #' @param main.assay the name of the main assay
+#' @param verbose verbose
 #'
 #' @rdname merge
 #' @aliases merge
 #' @method merge VoltRon
 #' @importFrom methods new
 #'
 #' @export
-merge.VoltRon <- function(object, object_list, samples = NULL, main.assay = NULL) {
+merge.VoltRon <- function(object, object_list, samples = NULL, main.assay = NULL, verbose = TRUE) {
 
   # combine all elements
   if(!is.list(object_list))
@@ -1080,12 +1081,14 @@ merge.VoltRon <- function(object, object_list, samples = NULL, main.assay = NULL
   sample.metadata <- merge_sampleMetadata(sample.metadata_list)
 
   # merge metadata and sample metadata
-  message("Merging metadata ...")
+  if(verbose)
+    message("Merging metadata ...")
   metadata_list <- lapply(object_list, function(x) slot(x, name = "metadata"))
   metadata <- merge(metadata_list[[1]], metadata_list[-1])
 
   # combine samples and rename layers
-  message("Merging blocks and layers ...")
+  if(verbose)
+    message("Merging blocks and layers ...")
   listofSamples <- NULL
   for(i in 1:length(object_list)){
     cur_object <- object_list[[i]]@samples

R/spatial.R

@@ -19,6 +19,7 @@ NULL
 #' @param k number of neighbors for kNN.
 #' @param radius When \code{method = "radius"} selected, determines the radius of a neighborhood ball around each spatial point.
 #' @param graph.key the name of the graph.
+#' @param verbose verbose
 #'
 #' @importFrom igraph add_edges simplify make_empty_graph vertices
 #' @importFrom RCDT delaunay
@@ -34,7 +35,8 @@ getSpatialNeighbors <- function(object,
                                 method = "delaunay", 
                                 k = 10, 
                                 radius = numeric(0), 
-                                graph.key = method){
+                                graph.key = method, 
+                                verbose = TRUE){
 
   # get coordinates
   spatialpoints <- vrSpatialPoints(object, assay = assay)
@@ -56,7 +58,8 @@ getSpatialNeighbors <- function(object,
     if(!is.null(group.by) && !is.null(group.ids)){
 
       # metadata
-      message("Calculating Spatial Neighbors with group.by='", group.by, "' and group.ids='", paste(group.ids, collapse = ","), "'\n")
+      if(verbose)
+        message("Calculating Spatial Neighbors with group.by='", group.by, "' and group.ids='", paste(group.ids, collapse = ","), "'\n")
       metadata = Metadata(object, assay = assy)
       if(!group.by %in% colnames(metadata))
         stop("The column '", group.by, "' was not found in the metadata!")
@@ -153,10 +156,11 @@ getSpatialNeighbors <- function(object,
 #' @param graph.type the type of graph to determine spatial neighborhood
 #' @param num.sim the number of simulations
 #' @param seed seed
+#' @param verbose verbose
 #'
 #' @export
 #'
-vrNeighbourhoodEnrichment <- function(object, assay = NULL, group.by = NULL, graph.type = "delaunay", num.sim = 1000, seed = 1){
+vrNeighbourhoodEnrichment <- function(object, assay = NULL, group.by = NULL, graph.type = "delaunay", num.sim = 1000, seed = 1, verbose = TRUE){
 
   # set the seed
   set.seed(seed)
@@ -174,7 +178,8 @@ vrNeighbourhoodEnrichment <- function(object, assay = NULL, group.by = NULL, gra
   # test for each assay
   neigh_results <- list()
   for(assy in assay_names){
-    message("Testing Neighborhood Enrichment of '", group.by ,"' for '", assy, "'")
+    if(verbose)
+      message("Testing Neighborhood Enrichment of '", group.by ,"' for '", assy, "'")
     object_subset <- subset(object, assays = assy)
     neigh_results[[assy]] <- vrNeighbourhoodEnrichmentSingle(object_subset, group.by = group.by, graph.type = graph.type,
                                                              num.sim = num.sim, seed = seed)
@@ -277,13 +282,14 @@ vrNeighbourhoodEnrichmentSingle <- function(object, group.by = NULL, graph.type
 #' @param alpha.value the alpha value for the hot spot analysis test. Default is 0.01
 #' @param norm if TRUE, the normalized data is used
 #' @param seed seed
+#' @param verbose verbose
 #' 
 #' @importFrom Matrix rowSums
 #' @importFrom igraph as_adjacency_matrix
 #' @importFrom stats pnorm
 #'
 #' @export
-getHotSpotAnalysis <- function(object, assay = NULL, method = "Getis-Ord", features, graph.type = "delaunay", alpha.value = 0.01, norm = TRUE, seed = 1){
+getHotSpotAnalysis <- function(object, assay = NULL, method = "Getis-Ord", features, graph.type = "delaunay", alpha.value = 0.01, norm = TRUE, seed = 1, verbose = TRUE){
 
   # set the seed
   set.seed(seed)
@@ -311,7 +317,8 @@ getHotSpotAnalysis <- function(object, assay = NULL, method = "Getis-Ord", featu
   for(assy in assay_names){
 
     # verbose
-    message("Running Hot Spot Analysis with '", method, "' for '", assy, "'")
+    if(verbose)
+      message("Running Hot Spot Analysis with '", method, "' for '", assy, "'")
 
     # get related data 
     graph <- vrGraph(object, assay = assy, graph.type = graph.type)