Merge pull request #209 from drieslab/dev

chore: catch up to dev
drieslab · Jul 15, 2024 · 3458c24 · 3458c24
2 parents 9ad5829 + 1acad0c
commit 3458c24
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Showing 12 changed files with 44 additions and 28 deletions.
diff --git 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
@@ -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/auxilliary.R b/R/auxilliary.R
@@ -792,7 +792,7 @@ create_average_DT <- function(gobject,
         expression_values,
         unique(c("normalized", "scaled", "custom", expression_values))
     )
-    expr_data <- get_expression_values(
+    expr_data <- getExpression(
         gobject = gobject,
         spat_unit = spat_unit,
         feat_type = feat_type,
@@ -863,7 +863,7 @@ create_average_detection_DT <- function(gobject,
         expression_values,
         unique(c("normalized", "scaled", "custom", expression_values))
     )
-    expr_data <- get_expression_values(
+    expr_data <- getExpression(
         gobject = gobject,
         spat_unit = spat_unit,
         feat_type = feat_type,
@@ -1081,7 +1081,7 @@ calculateMetaTable <- function(gobject,
             expression_values
         ))
     )
-    expr_values <- get_expression_values(
+    expr_values <- getExpression(
         gobject = gobject,
         spat_unit = spat_unit,
         feat_type = feat_type,
@@ -1396,7 +1396,7 @@ createMetafeats <- function(gobject,
             expression_values
         ))
     )
-    exprobj <- get_expression_values(
+    exprobj <- getExpression(
         gobject = gobject,
         spat_unit = spat_unit,
         feat_type = feat_type,

diff --git 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
@@ -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/methods-initialize.R b/R/methods-initialize.R
@@ -272,7 +272,7 @@ setMethod("initialize", signature("giotto"), function(.Object, ...) {
             if (!is.null(avail_expr)) {
                 if (nrow(avail_expr[spat_unit == spatial_unit &
                     feat_type == feature_type]) != 0L) {
-                    provenance <- prov(get_expression_values(
+                    provenance <- prov(getExpression(
                         gobject = .Object,
                         spat_unit = spatial_unit,
                         feat_type = feature_type,

diff --git 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
@@ -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
@@ -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]],

diff --git a/tests/testthat/test-auxiliary.R b/tests/testthat/test-auxiliary.R
@@ -16,6 +16,7 @@ m <- matrix(
 e <- exprObj(
     exprMat = m,
     spat_unit = "cell",
+    provenance = "cell",
     feat_type = "test_feat",
     name = "test"
 )
@@ -36,13 +37,15 @@ df_clus_weight <- data.frame(
 )
 
 test_that("createMetafeat can calculate mean values", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     expect_m <- matrix(rep(c(2, 5, 8), 3), nrow = 3)
 
     g <- createMetafeats(
         g, stat = "mean",
         expression_values = "test",
         feat_clusters = num_vec_clus,
-        name = "chara_vec_mean"
+        name = "chara_vec_mean",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "chara_vec_mean",
                                 output = "data.table")
@@ -55,7 +58,8 @@ test_that("createMetafeat can calculate mean values", {
         g, stat = "mean",
         expression_values = "test",
         feat_clusters = df_clus,
-        name = "df_mean"
+        name = "df_mean",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "df_mean", output = "data.table")
 
@@ -65,13 +69,15 @@ test_that("createMetafeat can calculate mean values", {
 })
 
 test_that("createMetafeat can calculate sum values", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     expect_m <- matrix(c(6, 15, 24, 4, 10, 16, 2, 5, 8), nrow = 3)
 
     g <- createMetafeats(
         g, stat = "sum",
         expression_values = "test",
         feat_clusters = num_vec_clus,
-        name = "sum"
+        name = "sum",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "sum", output = "data.table")
 
@@ -81,13 +87,15 @@ test_that("createMetafeat can calculate sum values", {
 })
 
 test_that("createMetafeat can calculate min values", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     expect_m <- matrix(c(1L, 4L, 7L, 1L, 4L, 7L, 2L, 5L, 8L), nrow = 3)
 
     g <- createMetafeats(
         g, stat = "min",
         expression_values = "test",
         feat_clusters = num_vec_clus,
-        name = "min"
+        name = "min",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "min", output = "data.table")
 
@@ -97,13 +105,15 @@ test_that("createMetafeat can calculate min values", {
 })
 
 test_that("createMetafeat can calculate max values", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     expect_m <- matrix(c(3L, 6L, 9L, 3L, 6L, 9L, 2L, 5L, 8L), nrow = 3)
 
     g <- createMetafeats(
         g, stat = "max",
         expression_values = "test",
         feat_clusters = num_vec_clus,
-        name = "max"
+        name = "max",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "max", output = "data.table")
 
@@ -113,13 +123,15 @@ test_that("createMetafeat can calculate max values", {
 })
 
 test_that("createMetafeat can use weights", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     expect_m <- matrix(c(4, 10, 16, 0.4, 1.3, 2.2, 2, 5, 8), nrow = 3)
 
     g <- createMetafeats(
         g, stat = "mean",
         expression_values = "test",
         feat_clusters = df_clus_weight,
-        name = "weighted_means"
+        name = "weighted_means",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "weighted_means",
                                 output = "data.table")
@@ -130,14 +142,16 @@ test_that("createMetafeat can use weights", {
 })
 
 test_that("createMetafeat can use rescale", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     expect_m <- matrix(rep(c(0, 0.5, 1), 3), nrow = 3)
 
     g <- createMetafeats(
         g, stat = "mean",
         expression_values = "test",
         feat_clusters = num_vec_clus,
         rescale_to = c(0, 1),
-        name = "scaled_means"
+        name = "scaled_means",
+        verbose = FALSE
     )
     enr <- getSpatialEnrichment(g, name = "scaled_means",
                                 output = "data.table")

diff --git a/tests/testthat/test-save_load.R b/tests/testthat/test-save_load.R
@@ -3,13 +3,15 @@ g <- GiottoData::loadGiottoMini("viz")
 test <- tempdir()
 
 test_that("gobject can be saved and loaded - qs", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     saveGiotto(g, dir = test, method = "qs", overwrite = TRUE, verbose = FALSE)
     g2 <<- loadGiotto(file.path(test, "saveGiottoDir"))
 
     expect_true(methods::validObject(g2))
 })
 
 test_that("gobject an be ovewritten and loaded - qs", {
+    rlang::local_options(lifecycle_verbosity = "quiet")
     saveGiotto(g2, dir = test, method = "qs", overwrite = TRUE, verbose = FALSE)
     g3 <- loadGiotto(file.path(test, "saveGiottoDir"))
 

diff --git a/tests/testthat/test-slot_accessors.R b/tests/testthat/test-slot_accessors.R
@@ -20,7 +20,8 @@ test_that("Not found exprObj returns error", {
     expect_error(
         getExpression(giotto_object,
             spat_unit = "none",
-            feat_type = "none", values = "raw"
+            feat_type = "none", 
+            values = "raw"
         )
     )
 })
@@ -31,8 +32,7 @@ test_that("Not found CellMetadata returns error", {
         getCellMetadata(
             giotto_object,
             spat_unit = "none",
-            feat_type = "none",
-            values = "raw"
+            feat_type = "none"
         )
     )
 })