From 1f4a6ce556f8f28e3466b5ba9a481e655a28c32f Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Mon, 15 Jul 2024 14:31:52 -0400
Subject: [PATCH] chore: update expression accessor usage

`get_expression_values()` -> `getExpression()`
---
 R/NN_network.R       |  2 +-
 R/aggregate.R        |  2 +-
 R/interoperability.R | 12 ++++++------
 R/join.R             |  2 +-
 R/slot_accessors.R   |  4 ++--
 R/slot_check.R       |  2 +-
 R/slot_show.R        |  2 +-
 7 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/NN_network.R b/R/NN_network.R
index d14b4607..66cc7cdc 100644
--- a/R/NN_network.R
+++ b/R/NN_network.R
@@ -704,7 +704,7 @@ createNearestNetwork <- function(
                 expression_values
             ))
         )
-        expr_obj <- get_expression_values(
+        expr_obj <- getExpression(
             gobject = gobject,
             feat_type = feat_type,
             spat_unit = spat_unit,
diff --git a/R/aggregate.R b/R/aggregate.R
index 4b3f7fa2..e30e1ef7 100644
--- a/R/aggregate.R
+++ b/R/aggregate.R
@@ -1900,7 +1900,7 @@ aggregateStacksExpression <- function(gobject,
     # aggregate matrices
     matrix_list <- list()
     for (spat_unit in spat_units) {
-        mat <- get_expression_values(gobject,
+        mat <- getExpression(gobject,
             spat_unit = spat_unit,
             feat_type = feat_type,
             values = values,
diff --git a/R/interoperability.R b/R/interoperability.R
index 302d1342..30edf4bb 100644
--- a/R/interoperability.R
+++ b/R/interoperability.R
@@ -691,7 +691,7 @@ giottoToAnnData <- function(
 
             for (en in expr_names) {
                 if (en == "raw") {
-                    raw_x <- get_expression_values(
+                    raw_x <- getExpression(
                         gobject = gobject,
                         values = en,
                         spat_unit = su,
@@ -703,7 +703,7 @@ giottoToAnnData <- function(
                 } else {
                     ad_layer_name <- paste0(su, "_", ft, "_", en)
 
-                    x <- get_expression_values(
+                    x <- getExpression(
                         gobject = gobject,
                         values = en,
                         spat_unit = su,
@@ -1222,7 +1222,7 @@ giottoToSeuratV4 <- function(
         expr_use <- lapply(
             avail_expr[feat_type == assay_use, name],
             function(x) {
-                get_expression_values(
+                getExpression(
                     gobject = gobject,
                     spat_unit = spat_unit,
                     feat_type = assay_use,
@@ -1503,7 +1503,7 @@ giottoToSeuratV5 <- function(
         expr_use <- lapply(
             avail_expr[feat_type == assay_use, name],
             function(x) {
-                get_expression_values(
+                getExpression(
                     gobject = gobject,
                     spat_unit = spat_unit,
                     feat_type = assay_use,
@@ -2613,7 +2613,7 @@ giottoToSpatialExperiment <- function(giottoObj, verbose = TRUE) {
                     "' for spatial unit: '", spatialUnits[su], "'"
                 )
             }
-            exprMat <- get_expression_values(
+            exprMat <- getExpression(
                 gobject = giottoObj,
                 spat_unit = spatialUnits[su],
                 feat_type = giottoExpr[1]$feat_type,
@@ -2657,7 +2657,7 @@ giottoToSpatialExperiment <- function(giottoObj, verbose = TRUE) {
                         spatialUnits[su]
                     ),
                     withDimnames = FALSE
-                ) <- get_expression_values(
+                ) <- getExpression(
                     gobject = giottoObj,
                     spat_unit = spatialUnits[su],
                     feat_type = giottoExpr[i]$feat_type,
diff --git a/R/join.R b/R/join.R
index 5d3e886a..dbac99dd 100644
--- a/R/join.R
+++ b/R/join.R
@@ -647,7 +647,7 @@ joinGiottoObjects <- function(gobject_list,
     } else {
         for (exprObj_i in seq(nrow(avail_expr))) {
             expr_list <- lapply(updated_object_list, function(gobj) {
-                get_expression_values(
+                getExpression(
                     gobject = gobj,
                     spat_unit = avail_expr$spat_unit[[exprObj_i]],
                     feat_type = avail_expr$feat_type[[exprObj_i]],
diff --git a/R/slot_accessors.R b/R/slot_accessors.R
index 597df24a..ec793e8c 100644
--- a/R/slot_accessors.R
+++ b/R/slot_accessors.R
@@ -284,7 +284,7 @@ set_cell_id <- function(gobject,
         # get cell ID values
         if (spat_unit %in% expr_avail$spat_unit) { # preferred from expression
 
-            cell_IDs <- spatIDs(get_expression_values(
+            cell_IDs <- spatIDs(getExpression(
                 gobject = gobject,
                 spat_unit = spat_unit,
                 feat_type = expr_avail$feat_type[[1L]],
@@ -424,7 +424,7 @@ set_feat_id <- function(gobject,
 
         if (feat_type %in% expr_avail$feat_type) { # preferred from expression
 
-            feat_IDs <- featIDs(get_expression_values(
+            feat_IDs <- featIDs(getExpression(
                 gobject = gobject,
                 spat_unit = expr_avail$spat_unit[[1L]],
                 feat_type = feat_type,
diff --git a/R/slot_check.R b/R/slot_check.R
index 1d94879d..7bd01032 100644
--- a/R/slot_check.R
+++ b/R/slot_check.R
@@ -178,7 +178,7 @@
             }
 
             if (!nrow(avail_ex[spat_unit == su_i & feat_type == ft_i]) == 0L) {
-                IDs <- featIDs(get_expression_values(
+                IDs <- featIDs(getExpression(
                     gobject = gobject,
                     spat_unit = su_i,
                     feat_type = ft_i,
diff --git a/R/slot_show.R b/R/slot_show.R
index d34e82ac..3f223a36 100644
--- a/R/slot_show.R
+++ b/R/slot_show.R
@@ -33,7 +33,7 @@ showGiottoExpression <- function(gobject, nrows = 4, ncols = 4) {
         objPrints <- list()
         for (obj_i in seq(nrow(available_data))) {
             # get object
-            dataObj <- get_expression_values(
+            dataObj <- getExpression(
                 gobject = gobject,
                 values = available_data$name[[obj_i]],
                 spat_unit = available_data$spat_unit[[obj_i]],