chore: update deprecated accessors

drieslab · Sep 12, 2024 · efdf9c0 · efdf9c0
1 parent 3b738f7
commit efdf9c0
Show file tree

Hide file tree

Showing 15 changed files with 178 additions and 215 deletions.
diff --git a/R/ONTraC_wrapper.R b/R/ONTraC_wrapper.R
@@ -398,7 +398,7 @@ plotNicheClusterConnectivity <- function( # nolint: object_name_linter.
   )
   gpl <- gpl + ggraph::scale_edge_alpha(range = c(0.1, 1))
   gpl <- gpl + ggraph::scale_edge_colour_gradientn(
-    colours = RColorBrewer::brewer.pal(9, "Reds"),
+    colours = getColors("Reds", 9, src = "RColorBrewer"),
     name = "Value"
   )
 
@@ -764,4 +764,4 @@ plotCellTypeNTScore <- function(gobject, # nolint: object_name_linter.
     save_param = save_param,
     else_return = NULL
   ))
-}
+}
diff --git a/R/auxiliary_giotto.R b/R/auxiliary_giotto.R
@@ -933,19 +933,12 @@ filterGiotto <- function(
     )
 
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-    gobject <- set_expression_values(
-        gobject = gobject,
-        values = norm_expr
-    )
-
-    gobject <- set_expression_values(
-        gobject = gobject,
-        values = norm_scaled_expr
-    )
+    gobject <- setGiotto(gobject, norm_expr, initialize = FALSE)
+    gobject <- setGiotto(gobject, norm_scaled_expr, initialize = FALSE)
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
     ## 6. return Giotto object
-    return(gobject)
+    return(initialize(gobject))
 }
 
 
@@ -991,13 +984,9 @@ filterGiotto <- function(
     )
 
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-    gobject <- set_expression_values(
-        gobject = gobject,
-        values = norm_feats_cells
-    )
+    gobject <- setGiotto(giotto, norm_feats_cells)
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
-
     return(gobject)
 }
 
@@ -1088,10 +1077,7 @@ filterGiotto <- function(
     )
 
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-    gobject <- set_expression_values(
-        gobject = gobject,
-        values = z
-    )
+    gobject <- setGiotto(gobject, z)
     ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
     return(gobject)
@@ -1391,10 +1377,7 @@ adjustGiottoMatrix <- function(
         )
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_expression_values(
-            gobject = gobject,
-            values = adjusted_matrix
-        )
+        gobject <- setGiotto(gobject, adjusted_matrix)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
         ## update parameters used ##
@@ -1456,14 +1439,14 @@ processGiotto <- function(
         adjust_params = list(),
         verbose = TRUE) {
     # filter Giotto
-    if (verbose == TRUE) message("1. start filter step")
+    vmsg(.v = verbose, "1. start filter step")
     if (!inherits(filter_params, "list")) {
         stop("filter_params need to be a list of parameters for filterGiotto")
     }
     gobject <- do.call("filterGiotto", c(gobject = gobject, filter_params))
 
     # normalize Giotto
-    if (verbose == TRUE) message("2. start normalization step")
+    vmsg(.v = verbose, "2. start normalization step")
     if (!inherits(norm_params, "list")) {
         stop("norm_params need to be a list of parameters for normalizeGiotto")
     }
@@ -1623,10 +1606,7 @@ addFeatStatistics <- function(
                 "mean_expr_det"
             ) := NULL]
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-            gobject <- set_feature_metadata(gobject,
-                metadata = feat_metadata,
-                verbose = FALSE
-            )
+            gobject <- setGiotto(gobject, feat_metadata, verbose = FALSE)
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
         }
 

diff --git a/R/clustering.R b/R/clustering.R
@@ -1278,7 +1278,7 @@ doKmeans <- function(
     if(!is.null(dim_reduction_to_use)) {
 
       # use only available dimensions if dimensions < dimensions_to_use
-      dim_coord <- get_dimReduction(
+      dim_coord <- getDimReduction(
         gobject = gobject,
         spat_unit = spat_unit,
         feat_type = feat_type,

diff --git a/R/convenience_cosmx.R b/R/convenience_cosmx.R
@@ -1645,7 +1645,7 @@ createGiottoCosMxObject <- function(
         provenance = "cell_agg"
     )
 
-    cosmx_gobject <- set_expression_values(cosmx_gobject, values = s4_expr)
+    cosmx_gobject <- setGiotto(cosmx_gobject, s4_expr)
 
     # Add spatial locations
     if (isTRUE(verbose)) wrap_msg(
@@ -1669,9 +1669,8 @@ createGiottoCosMxObject <- function(
         provenance = "cell_agg"
     )
 
-    cosmx_gobject <- set_spatial_locations(cosmx_gobject, spatlocs = locsObj)
-    cosmx_gobject <- set_spatial_locations(cosmx_gobject,
-                                           spatlocs = locsObj_fov)
+    cosmx_gobject <- setGiotto(cosmx_gobject, locsObj, initialize = FALSE)
+    cosmx_gobject <- setGiotto(cosmx_gobject, locsObj_fov, initialize = FALSE)
 
     # initialize cell and feat IDs and metadata slots for 'cell_agg' spat_unit
     agg_cell_ID <- colnames(s4_expr[])

diff --git a/R/dimension_reduction.R b/R/dimension_reduction.R
@@ -541,9 +541,7 @@ runPCA <- function(
         )
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_dimReduction(
-            gobject = gobject, dimObject = dimObject, verbose = verbose
-        )
+        gobject <- setGiotto(gobject, dimObject, verbose = verbose)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 
@@ -945,7 +943,7 @@ runPCAprojection <- function(
         )
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_dimReduction(gobject = gobject, dimObject = dimObject)
+        gobject <- setGiotto(gobject, dimObject, verbose = verbose)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 
@@ -1349,7 +1347,7 @@ runPCAprojectionBatch <- function(
         )
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_dimReduction(gobject = gobject, dimObject = dimObject)
+        gobject <- setGiotto(gobject, dimObject, verbose = verbose)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 
@@ -2168,7 +2166,7 @@ runUMAP <- function(
         ## using dimension reduction ##
         if (!is.null(dim_reduction_to_use)) {
             ## TODO: check if reduction exists
-            dimObj_to_use <- get_dimReduction(
+            dimObj_to_use <- getDimReduction(
                 gobject = gobject,
                 spat_unit = spat_unit,
                 feat_type = feat_type,
@@ -2291,10 +2289,7 @@ runUMAP <- function(
 
 
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-            gobject <- set_dimReduction(
-                gobject = gobject,
-                dimObject = dimObject
-            )
+            gobject <- setGiotto(gobject, dimObject, verbose = verbose)
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 
@@ -2566,7 +2561,7 @@ runUMAPprojection <- function(
 
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_dimReduction(gobject = gobject, dimObject = dimObject)
+        gobject <- setGiotto(gobject, dimObject, verbose = verbose)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
         ## update parameters used ##
@@ -2794,10 +2789,7 @@ runtSNE <- function(
             )
 
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-            gobject <- set_dimReduction(
-                gobject = gobject,
-                dimObject = dimObject
-            )
+            gobject <- setGiotto(gobject, dimObject, verbose = verbose)
             ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
             ## update parameters used ##
@@ -2931,7 +2923,7 @@ runGiottoHarmony <- function(
     ## using dimension reduction ##
     if (!is.null(dim_reduction_to_use)) {
         ## TODO: check if reduction exists
-        matrix_to_use <- get_dimReduction(
+        matrix_to_use <- getDimReduction(
             gobject = gobject,
             spat_unit = spat_unit,
             feat_type = feat_type,
@@ -3000,14 +2992,14 @@ runGiottoHarmony <- function(
     colnames(harmony_results) <- paste0("Dim.", seq_len(ncol(harmony_results)))
     rownames(harmony_results) <- rownames(matrix_to_use)
 
-    harmdimObject <- create_dim_obj(
+    harmdimObject <- createDimObj(
+        coordinates = harmony_results,
         name = name,
         spat_unit = spat_unit,
         feat_type = feat_type,
-        provenance = provenance,
+        method = "harmony",
         reduction = "cells", # set to spat_unit?
-        reduction_method = "harmony",
-        coordinates = harmony_results,
+        provenance = provenance,
         misc = NULL
     )
 
@@ -3029,10 +3021,7 @@ runGiottoHarmony <- function(
         }
 
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
-        gobject <- set_dimReduction(
-            gobject = gobject,
-            dimObject = harmdimObject
-        )
+        gobject <- setGiotto(gobject, harmdimObject, verbose = verbose)
         ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
 
 

diff --git a/R/giotto_viewer.R b/R/giotto_viewer.R
@@ -212,9 +212,10 @@ exportGiottoViewer <- function(
 
     # data.table variables
     sdimx <- sdimy <- NULL
-    spatial_location <- get_spatial_locations(
+    spatial_location <- getSpatialLocations(
         gobject = gobject,
-        spat_loc_name = spat_loc_name
+        spat_unit = spat_unit,
+        name = spat_loc_name
     )
     spatial_location <- spatial_location[, .(sdimx, sdimy)]
     write.table(spatial_location,
@@ -241,6 +242,7 @@ exportGiottoViewer <- function(
         cell_metadata <- combineMetadata(
             gobject = gobject,
             feat_type = feat,
+            spat_unit = spat_unit,
             spat_enr_names = spat_enr_names
         )
 
@@ -361,11 +363,12 @@ exportGiottoViewer <- function(
     values <- match.arg(expression_values, unique(c("scaled", "normalized", "custom", expression_values)))
 
     for (feat in feat_type) {
-        expr_values <- get_expression_values(
+        expr_values <- getExpression(
             gobject = gobject,
             spat_unit = spat_unit,
             feat_type = feat,
-            values = values
+            values = values,
+            output = "matrix"
         )
         expr_values <- as.matrix(expr_values)