339 migrate to teal data@main (#342)

Fixes #339 Part of - insightsengineering/nestdevs-tasks#41 - insightsengineering/teal.data#184 Partner of - insightsengineering/teal.modules.clinical#845 - insightsengineering/teal.modules.general#592 - insightsengineering/teal.modules.helios#103 --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: vedhav <[email protected]>
insightsengineering · Nov 20, 2023 · fd679d9 · fd679d9
1 parent 2b1ea05
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,7 @@ Depends:
     ggplot2,
     R (>= 3.6),
     shiny,
-    teal (>= 0.14.0)
+    teal (>= 0.14.0.9019)
 Imports:
     checkmate,
     DT,
@@ -47,7 +47,7 @@ Imports:
     stats,
     stringr,
     SummarizedExperiment,
-    teal.data (>= 0.3.0),
+    teal.data (>= 0.3.0.9010),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),

diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,10 @@
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.
 * Disabled the select input for `assaySpec` and `adtteSpec` when there are no options available.
 
+### Enhancements
+
+* Updated the documentation and vignettes with the new way of specifying data for `teal::init()`. The `data` argument accepts `teal_data` object.
+
 # teal.modules.hermes 0.1.5
 
 ### Bug Fixes

diff --git a/R/adtteSpec.R b/R/adtteSpec.R
@@ -208,19 +208,15 @@ adtteSpecInput <- function(inputId, # nolint
 #' }
 #'
 #' my_app <- function() {
-#'   mae <- hermes::multi_assay_experiment
-#'   adtte <- teal.modules.hermes::rADTTE %>%
-#'     dplyr::mutate(is_event = .data$CNSR == 0)
-#'
-#'   data <- teal_data(
-#'     dataset(
-#'       "ADTTE",
-#'       adtte,
-#'       code = "adtte <- teal.modules.hermes::rADTTE
-#'         dplyr::mutate(is_event = .data$CNSR == 0)"
-#'     ),
-#'     dataset("MAE", mae)
-#'   )
+#'   data <- teal_data()
+#'   data <- within(data, {
+#'     ADTTE <- teal.modules.hermes::rADTTE %>%
+#'       dplyr::mutate(is_event = .data$CNSR == 0)
+#'     MAE <- hermes::multi_assay_experiment
+#'   })
+#'   datanames <- c("ADTTE", "MAE")
+#'   datanames(data) <- datanames
+#'   join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
 #'   app <- init(
 #'     data = data,

diff --git a/R/assaySpec.R b/R/assaySpec.R
@@ -83,10 +83,7 @@ assaySpecInput <- function(inputId, # nolint
 #' }
 #'
 #' my_app <- function() {
-#'   mae <- hermes::multi_assay_experiment
-#'   mae_name <- "MAE"
-#'   mae_data <- dataset(mae_name, mae)
-#'   data <- teal_data(mae_data)
+#'   data <- teal_data(MAE = hermes::multi_assay_experiment)
 #'   app <- init(
 #'     data = data,
 #'     modules = modules(

diff --git a/R/barplot.R b/R/barplot.R
@@ -12,9 +12,7 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' mae_data <- dataset("MAE", mae)
-#' data <- teal_data(mae_data)
+#' data <- teal_data(MAE = hermes::multi_assay_experiment)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -246,9 +244,7 @@ srv_g_barplot <- function(id,
 #'   sample_tm_g_barplot()
 #' }
 sample_tm_g_barplot <- function() {
-  mae <- hermes::multi_assay_experiment
-  mae_data <- teal.data::dataset("MAE", mae)
-  data <- teal.data::teal_data(mae_data)
+  data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(

diff --git a/R/boxplot.R b/R/boxplot.R
@@ -12,9 +12,7 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' mae_data <- dataset("MAE", mae)
-#' data <- teal_data(mae_data)
+#' data <- teal_data(MAE = hermes::multi_assay_experiment)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -247,9 +245,7 @@ srv_g_boxplot <- function(id,
 #'   sample_tm_g_boxplot()
 #' }
 sample_tm_g_boxplot <- function() {
-  mae <- hermes::multi_assay_experiment
-  mae_data <- teal.data::dataset("MAE", mae)
-  data <- teal.data::teal_data(mae_data)
+  data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(

diff --git a/R/experimentSpec.R b/R/experimentSpec.R
@@ -183,19 +183,16 @@ h_gene_data <- function(object, name_annotation) {
 #' }
 #'
 #' my_app <- function() {
-#'   mae <- hermes::multi_assay_experiment
-#'   mae_name <- "MAE"
-#'   mae_data <- dataset(mae_name, mae)
-#'   data <- teal_data(mae_data)
+#'   data <- teal_data(MAE = hermes::multi_assay_experiment)
 #'   app <- init(
 #'     data = data,
 #'     modules = modules(
 #'       module(
 #'         label = "experimentSpec example",
 #'         server = server,
-#'         server_args = list(mae_name = mae_name),
+#'         server_args = list(mae_name = "MAE"),
 #'         ui = ui,
-#'         ui_args = list(mae_name = mae_name),
+#'         ui_args = list(mae_name = "MAE"),
 #'         datanames = "all"
 #'       )
 #'     )

diff --git a/R/forestplot.R b/R/forestplot.R
@@ -11,19 +11,16 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' adtte <- teal.modules.hermes::rADTTE %>%
-#'   dplyr::mutate(is_event = (.data$CNSR == 0))
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADTTE <- teal.modules.hermes::rADTTE %>%
+#'     dplyr::mutate(is_event = .data$CNSR == 0)
+#'   MAE <- hermes::multi_assay_experiment
+#' })
+#' datanames <- c("ADTTE", "MAE")
+#' datanames(data) <- datanames
+#' join_keys(data)["ADTTE", "ADTTE"] <- c("STUDYID", "USUBJID", "PARAMCD")
 #'
-#' data <- teal_data(
-#'   dataset(
-#'     "ADTTE",
-#'     adtte,
-#'     code = "adtte <- teal.modules.hermes::rADTTE %>%
-#'       dplyr::mutate(is_event = (.data$CNSR == 0))"
-#'   ),
-#'   dataset("MAE", mae)
-#' )
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -286,20 +283,15 @@ srv_g_forest_tte <- function(id,
 #'   sample_tm_g_forest_tte()
 #' }
 sample_tm_g_forest_tte <- function() { # nolint
-
-  mae <- hermes::multi_assay_experiment
-  adtte <- teal.modules.hermes::rADTTE %>%
-    dplyr::mutate(is_event = .data$CNSR == 0)
-
-  data <- teal.data::teal_data(
-    teal.data::dataset(
-      "ADTTE",
-      adtte,
-      code = "adtte <- teal.modules.hermes::rADTTE %>%
-        dplyr::mutate(is_event = .data$CNSR == 0)"
-    ),
-    teal.data::dataset("MAE", mae)
-  )
+  data <- teal_data()
+  data <- within(data, {
+    ADTTE <- teal.modules.hermes::rADTTE %>% # nolint
+      dplyr::mutate(is_event = .data$CNSR == 0)
+    MAE <- hermes::multi_assay_experiment # nolint
+  })
+  datanames <- c("ADTTE", "MAE")
+  datanames(data) <- datanames
+  join_keys(data)["ADTTE", "ADTTE"] <- c("STUDYID", "USUBJID", "PARAMCD")
 
   app <- teal::init(
     data = data,

diff --git a/R/geneSpec.R b/R/geneSpec.R
@@ -266,9 +266,7 @@ h_parse_genes <- function(words, choices) {
 #' }
 #' funs <- list(mean = colMeans)
 #' my_app <- function() {
-#'   mae <- hermes::multi_assay_experiment
-#'   mae_data <- dataset("MAE", mae)
-#'   data <- teal_data(mae_data)
+#'   data <- teal_data(MAE = hermes::multi_assay_experiment)
 #'   app <- init(
 #'     data = data,
 #'     modules = modules(

diff --git a/R/km.R b/R/km.R
@@ -12,19 +12,16 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' adtte <- teal.modules.hermes::rADTTE %>%
-#'   dplyr::mutate(is_event = (.data$CNSR == 0))
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADTTE <- teal.modules.hermes::rADTTE %>%
+#'     dplyr::mutate(is_event = .data$CNSR == 0)
+#'   MAE <- hermes::multi_assay_experiment
+#' })
+#' datanames <- c("ADTTE", "MAE")
+#' datanames(data) <- datanames
+#' join_keys(data)["ADTTE", "ADTTE"] <- c("STUDYID", "USUBJID", "PARAMCD")
 #'
-#' data <- teal_data(
-#'   dataset(
-#'     "ADTTE",
-#'     adtte,
-#'     code = "adtte <- teal.modules.hermes::rADTTE %>%
-#'       dplyr::mutate(is_event = (.data$CNSR == 0))"
-#'   ),
-#'   dataset("MAE", mae)
-#' )
 #'
 #' modules <- modules(
 #'   tm_g_km(
@@ -278,20 +275,15 @@ srv_g_km <- function(id,
 #'   sample_tm_g_km()
 #' }
 sample_tm_g_km <- function() { # nolint
-
-  mae <- hermes::multi_assay_experiment
-  adtte <- teal.modules.hermes::rADTTE %>%
-    dplyr::mutate(is_event = (.data$CNSR == 0))
-
-  data <- teal.data::teal_data(
-    teal.data::dataset(
-      "ADTTE",
-      adtte,
-      code = "adtte <- teal.modules.hermes::rADTTE %>%
-        dplyr::mutate(is_event = (.data$CNSR == 0))"
-    ),
-    teal.data::dataset("MAE", mae)
-  )
+  data <- teal_data()
+  data <- within(data, {
+    ADTTE <- teal.modules.hermes::rADTTE %>% # nolint
+      dplyr::mutate(is_event = .data$CNSR == 0)
+    MAE <- hermes::multi_assay_experiment # nolint
+  })
+  datanames <- c("ADTTE", "MAE")
+  datanames(data) <- datanames
+  join_keys(data)["ADTTE", "ADTTE"] <- c("STUDYID", "USUBJID", "PARAMCD")
 
   modules <- teal::modules(
     tm_g_km(

diff --git a/R/pca.R b/R/pca.R
@@ -12,9 +12,7 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' mae_data <- dataset("MAE", mae)
-#' data <- teal_data(mae_data)
+#' data <- teal_data(MAE = hermes::multi_assay_experiment)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -451,9 +449,7 @@ srv_g_pca <- function(id,
 #'   sample_tm_g_pca()
 #' }
 sample_tm_g_pca <- function() {
-  mae <- hermes::multi_assay_experiment
-  mae_data <- teal.data::dataset("MAE", mae)
-  data <- teal.data::teal_data(mae_data)
+  data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(

diff --git a/R/quality.R b/R/quality.R
@@ -66,9 +66,7 @@ heatmap_plot <- function(object, assay_name) {
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' mae_data <- dataset("MAE", mae)
-#' data <- teal_data(mae_data)
+#' data <- teal_data(MAE = hermes::multi_assay_experiment)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -418,9 +416,7 @@ srv_g_quality <- function(id,
 #'   sample_tm_g_quality()
 #' }
 sample_tm_g_quality <- function() {
-  mae <- hermes::multi_assay_experiment
-  mae_data <- teal.data::dataset("MAE", mae)
-  data <- teal.data::teal_data(mae_data)
+  data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(

diff --git a/R/sampleVarSpec.R b/R/sampleVarSpec.R
@@ -245,9 +245,7 @@ validate_n_levels <- function(x, name, n_levels) {
 #'   })
 #' }
 #' my_app <- function() {
-#'   mae <- hermes::multi_assay_experiment
-#'   mae_data <- dataset("MAE", mae)
-#'   data <- teal_data(mae_data)
+#'   data <- teal_data(MAE = hermes::multi_assay_experiment)
 #'   app <- init(
 #'     data = data,
 #'     modules = modules(
@@ -419,9 +417,9 @@ sampleVarSpecServer <- function(id, # nolint
 
           old_values <- names(assign_lists[[experiment_name]][[sample_var]])
           if (!is.null(old_values) &&
-            length(old_values) == length(sample_var_levels) &&
-            all(sort(old_values) == sort(sample_var_levels))) {
-            selected_groups <- assign_lists[[experiment_name]][[sample_var]]
+            length(old_values) == length(sample_var_levels) && # nolint
+            all(sort(old_values) == sort(sample_var_levels))) { # nolint
+            selected_groups <- assign_lists[[experiment_name]][[sample_var]] # nolint
           }
 
           showModal(combModal(

diff --git a/R/scatterplot.R b/R/scatterplot.R
@@ -12,9 +12,7 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' mae_data <- dataset("MAE", mae)
-#' data <- teal_data(mae_data)
+#' data <- teal_data(MAE = hermes::multi_assay_experiment)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -245,9 +243,7 @@ srv_g_scatterplot <- function(id,
 #'   sample_tm_g_scatterplot()
 #' }
 sample_tm_g_scatterplot <- function() {
-  mae <- hermes::multi_assay_experiment
-  mae_data <- teal.data::dataset("MAE", mae)
-  data <- teal.data::teal_data(mae_data)
+  data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(

diff --git a/R/volcanoplot.R b/R/volcanoplot.R
@@ -12,9 +12,7 @@
 #' @export
 #'
 #' @examples
-#' mae <- hermes::multi_assay_experiment
-#' mae_data <- dataset("MAE", mae)
-#' data <- teal_data(mae_data)
+#' data <- teal_data(MAE = hermes::multi_assay_experiment)
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -267,9 +265,7 @@ srv_g_volcanoplot <- function(id,
 #'   sample_tm_g_volcanoplot()
 #' }
 sample_tm_g_volcanoplot <- function() {
-  mae <- hermes::multi_assay_experiment
-  mae_data <- teal.data::dataset("MAE", mae)
-  data <- teal.data::teal_data(mae_data)
+  data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(