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339 migrate to teal data@main #342

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merged 37 commits into from
Nov 20, 2023
Merged

339 migrate to teal data@main #342

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eabfa41
reduce the content of WORDLIST
m7pr Jun 30, 2023
43d2341
merge
m7pr Jul 12, 2023
993fabc
Merge branch 'main' of https://github.com/insightsengineering/teal.mo…
m7pr Jul 28, 2023
bde2c1d
Merge branch 'main' of https://github.com/insightsengineering/teal.mo…
m7pr Nov 7, 2023
3d0566b
TealData to teal_data substitution
m7pr Nov 7, 2023
49dd4c8
fix joinkeys
m7pr Nov 7, 2023
5a5e121
update NEWS
m7pr Nov 8, 2023
33f85ef
rebuild examples
m7pr Nov 8, 2023
6c2ed19
fix one more example
m7pr Nov 8, 2023
afc314a
few more teal_data changes
m7pr Nov 8, 2023
5bf9f0b
join_keys() instead of data@joinkeys
m7pr Nov 8, 2023
904e4cc
bump teal.data
m7pr Nov 8, 2023
78f95d8
fix join keys
m7pr Nov 8, 2023
671f8be
missing pipe
m7pr Nov 8, 2023
98f00c7
fix code reproducibility using within
m7pr Nov 8, 2023
af31f6a
Merge 98f00c70c985c18b582d3a2f49df00f833dddb17 into 2b1ea056164819cbd…
m7pr Nov 8, 2023
e1ec8b8
[skip actions] Restyle files
github-actions[bot] Nov 8, 2023
2d4bd0f
import rlang and !!!
m7pr Nov 8, 2023
e7d461b
Merge branch '339_migrate_to_teal_data@main' of https://github.com/in…
m7pr Nov 8, 2023
4ee7b3a
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 8, 2023
4d19279
data@join_keys -> join_keys(data)
m7pr Nov 9, 2023
6fa22de
Merge 4d192794877520a30e237a4f36d497edc244f6de into 2b1ea056164819cbd…
m7pr Nov 9, 2023
500ae53
[skip actions] Restyle files
github-actions[bot] Nov 9, 2023
71f64d4
revert changes for design files
m7pr Nov 9, 2023
8f2e7ca
Merge branch '339_migrate_to_teal_data@main' of https://github.com/in…
m7pr Nov 9, 2023
07a8d41
[skip actions] Roxygen Man Pages Auto Update
dependabot-preview[bot] Nov 9, 2023
7de3979
add nolint
m7pr Nov 9, 2023
7a32b9d
Merge branch '339_migrate_to_teal_data@main' of https://github.com/in…
m7pr Nov 9, 2023
c45d12c
Merge 7a32b9dd1d475f68b1250d9e03deb26a074ed857 into 2b1ea056164819cbd…
m7pr Nov 9, 2023
0553764
[skip actions] Restyle files
github-actions[bot] Nov 9, 2023
ba3eb95
change !!!datanames to default_cdisc_join_keys[datanames]
m7pr Nov 14, 2023
7aa643a
Merge branch '339_migrate_to_teal_data@main' of https://github.com/in…
m7pr Nov 14, 2023
8067448
bump teal.data version
m7pr Nov 14, 2023
0bc4d93
remove rlang
m7pr Nov 14, 2023
43a3c9d
chore: replace `runApp` with `shinyApp`
vedhav Nov 17, 2023
347054d
chore: vbump
vedhav Nov 20, 2023
8e28189
fix: use proper keys for km and forest module
vedhav Nov 20, 2023
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -40,14 +40,15 @@ Imports:
lifecycle,
logger (>= 0.2.0),
MultiAssayExperiment,
rlang,
rtables (>= 0.5.1),
S4Vectors,
shinyRadioMatrix (>= 0.2.1),
shinyWidgets,
stats,
stringr,
SummarizedExperiment,
teal.data (>= 0.3.0),
teal.data (>= 0.3.0.9008),
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should be bumped to 0.4.0

teal.logger (>= 0.1.1),
teal.reporter (>= 0.2.0),
teal.widgets (>= 0.4.0),
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -72,3 +72,4 @@ import(teal)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,setListElement)
importFrom(lifecycle,deprecate_soft)
importFrom(rlang,`!!!`)
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4 changes: 4 additions & 0 deletions NEWS.md
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Expand Up @@ -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
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22 changes: 9 additions & 13 deletions R/adtteSpec.R
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Expand Up @@ -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
#' data@join_keys <- cdisc_join_keys(!!!datanames)
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#'
#' app <- init(
#' data = data,
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5 changes: 1 addition & 4 deletions R/assaySpec.R
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Expand Up @@ -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(
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8 changes: 2 additions & 6 deletions R/barplot.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
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8 changes: 2 additions & 6 deletions R/boxplot.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
9 changes: 3 additions & 6 deletions R/experimentSpec.R
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Expand Up @@ -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"
#' )
#' )
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44 changes: 18 additions & 26 deletions R/forestplot.R
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Expand Up @@ -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$CNSR == 0)
#' MAE <- hermes::multi_assay_experiment
#' })
#' datanames <- c("ADTTE", "MAE")
#' datanames(data) <- datanames
#' data@join_keys <- cdisc_join_keys(!!!datanames)
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#'
#' data <- teal_data(
#' dataset(
#' "ADTTE",
#' adtte,
#' code = "adtte <- teal.modules.hermes::rADTTE %>%
#' dplyr::mutate(is_event = (.data$CNSR == 0))"
#' ),
#' dataset("MAE", mae)
#' )
#' app <- init(
#' data = data,
#' modules = modules(
Expand Down Expand Up @@ -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$CNSR == 0)"
),
teal.data::dataset("MAE", mae)
)
data <- teal_data()
data <- within(data, {
ADTTE <- teal.modules.hermes::rADTTE %>%
dplyr::mutate(is_event = .data$CNSR == 0)
MAE <- hermes::multi_assay_experiment
})
datanames <- c("ADTTE", "MAE")
datanames(data) <- datanames
data@join_keys <- cdisc_join_keys(!!!datanames)
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app <- teal::init(
data = data,
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4 changes: 1 addition & 3 deletions R/geneSpec.R
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Expand Up @@ -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(
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44 changes: 18 additions & 26 deletions R/km.R
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Expand Up @@ -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
#' data@join_keys <- cdisc_join_keys(!!!datanames)
#'
#' 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(
Expand Down Expand Up @@ -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$CNSR == 0))"
),
teal.data::dataset("MAE", mae)
)
data <- teal_data()
data <- within(data, {
ADTTE <- teal.modules.hermes::rADTTE %>%
dplyr::mutate(is_event = .data$CNSR == 0)
MAE <- hermes::multi_assay_experiment
})
datanames <- c("ADTTE", "MAE")
datanames(data) <- datanames
data@join_keys <- cdisc_join_keys(!!!datanames)
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modules <- teal::modules(
tm_g_km(
Expand Down
1 change: 1 addition & 0 deletions R/package.R
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Expand Up @@ -10,4 +10,5 @@
#' @import teal
#' @importFrom S4Vectors setListElement DataFrame
#' @importFrom lifecycle deprecate_soft
#' @importFrom rlang `!!!`
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NULL
8 changes: 2 additions & 6 deletions R/pca.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
8 changes: 2 additions & 6 deletions R/quality.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
4 changes: 1 addition & 3 deletions R/sampleVarSpec.R
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Expand Up @@ -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(
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8 changes: 2 additions & 6 deletions R/scatterplot.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
8 changes: 2 additions & 6 deletions R/volcanoplot.R
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Expand Up @@ -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(
Expand Down Expand Up @@ -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(
Expand Down
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