diff --git a/R/FilteredDataset-utils.R b/R/FilteredDataset-utils.R index 3280415d0..afbda9a3e 100644 --- a/R/FilteredDataset-utils.R +++ b/R/FilteredDataset-utils.R @@ -51,32 +51,35 @@ #' shinyApp(ui, server) #' } #' -#' @examplesIf requireNamespace("MultiAssayExperiment") -#' # MAEFilteredDataset example -#' library(shiny) +#' @examples +#' \donttest{ +#' if (requireNamespace("MultiAssayExperiment", quietly = TRUE)) { +#' # MAEFilteredDataset example +#' library(shiny) #' -#' data(miniACC, package = "MultiAssayExperiment") +#' data(miniACC, package = "MultiAssayExperiment") #' -#' MAE_fd <- init_filtered_dataset(miniACC, "MAE") -#' ui <- fluidPage( -#' MAE_fd$ui_add(id = "add"), -#' MAE_fd$ui_active("dataset"), -#' verbatimTextOutput("call") -#' ) -#' server <- function(input, output, session) { -#' MAE_fd$srv_add(id = "add") -#' MAE_fd$srv_active(id = "dataset") -#' output$call <- renderText({ -#' paste( -#' vapply(MAE_fd$get_call(), deparse1, character(1), collapse = "\n"), -#' collapse = "\n" -#' ) -#' }) +#' MAE_fd <- init_filtered_dataset(miniACC, "MAE") +#' ui <- fluidPage( +#' MAE_fd$ui_add(id = "add"), +#' MAE_fd$ui_active("dataset"), +#' verbatimTextOutput("call") +#' ) +#' server <- function(input, output, session) { +#' MAE_fd$srv_add(id = "add") +#' MAE_fd$srv_active(id = "dataset") +#' output$call <- renderText({ +#' paste( +#' vapply(MAE_fd$get_call(), deparse1, character(1), collapse = "\n"), +#' collapse = "\n" +#' ) +#' }) +#' } +#' if (interactive()) { +#' shinyApp(ui, server) +#' } #' } -#' if (interactive()) { -#' shinyApp(ui, server) #' } -#' #' @keywords internal #' @export init_filtered_dataset <- function(dataset, # nolint diff --git a/R/filter_panel_api.R b/R/filter_panel_api.R index 47b05d415..861e08aef 100644 --- a/R/filter_panel_api.R +++ b/R/filter_panel_api.R @@ -60,56 +60,59 @@ #' # remove all states #' clear_filter_states(datasets) #' -#' @examplesIf requireNamespace("MultiAssayExperiment") -#' -#' # Requires MultiAssayExperiment from Bioconductor -#' data(miniACC, package = "MultiAssayExperiment") -#' -#' datasets <- init_filtered_data(list(mae = miniACC)) -#' fs <- teal_slices( -#' teal_slice( -#' dataname = "mae", varname = "years_to_birth", selected = c(30, 50), -#' keep_na = TRUE, keep_inf = FALSE -#' ), -#' teal_slice( -#' dataname = "mae", varname = "vital_status", selected = "1", -#' keep_na = FALSE -#' ), -#' teal_slice( -#' dataname = "mae", varname = "gender", selected = "female", -#' keep_na = TRUE -#' ), -#' teal_slice( -#' dataname = "mae", varname = "ARRAY_TYPE", selected = "", -#' keep_na = TRUE, experiment = "RPPAArray", arg = "subset" +#' @examples +#' \donttest{ +#' if (requireNamespace("MultiAssayExperiment", quietly = TRUE)) { +#' # Requires MultiAssayExperiment from Bioconductor +#' data(miniACC, package = "MultiAssayExperiment") +#' +#' datasets <- init_filtered_data(list(mae = miniACC)) +#' fs <- teal_slices( +#' teal_slice( +#' dataname = "mae", varname = "years_to_birth", selected = c(30, 50), +#' keep_na = TRUE, keep_inf = FALSE +#' ), +#' teal_slice( +#' dataname = "mae", varname = "vital_status", selected = "1", +#' keep_na = FALSE +#' ), +#' teal_slice( +#' dataname = "mae", varname = "gender", selected = "female", +#' keep_na = TRUE +#' ), +#' teal_slice( +#' dataname = "mae", varname = "ARRAY_TYPE", selected = "", +#' keep_na = TRUE, experiment = "RPPAArray", arg = "subset" +#' ) #' ) -#' ) #' -#' # set initial filter state -#' set_filter_state(datasets, filter = fs) +#' # set initial filter state +#' set_filter_state(datasets, filter = fs) #' -#' # get filter state -#' get_filter_state(datasets) +#' # get filter state +#' get_filter_state(datasets) #' -#' # modify filter state -#' set_filter_state( -#' datasets, -#' teal_slices( -#' teal_slice(dataname = "mae", varname = "years_to_birth", selected = c(40, 60)) +#' # modify filter state +#' set_filter_state( +#' datasets, +#' teal_slices( +#' teal_slice(dataname = "mae", varname = "years_to_birth", selected = c(40, 60)) +#' ) #' ) -#' ) #' -#' # remove specific filters -#' remove_filter_state( -#' datasets, -#' teal_slices( -#' teal_slice(dataname = "mae", varname = "years_to_birth"), -#' teal_slice(dataname = "mae", varname = "vital_status") +#' # remove specific filters +#' remove_filter_state( +#' datasets, +#' teal_slices( +#' teal_slice(dataname = "mae", varname = "years_to_birth"), +#' teal_slice(dataname = "mae", varname = "vital_status") +#' ) #' ) -#' ) #' -#' # remove all states -#' clear_filter_states(datasets) +#' # remove all states +#' clear_filter_states(datasets) +#' } +#' } NULL #' @rdname filter_state_api diff --git a/man/filter_state_api.Rd b/man/filter_state_api.Rd index 7af693e71..dcc739fff 100644 --- a/man/filter_state_api.Rd +++ b/man/filter_state_api.Rd @@ -76,57 +76,58 @@ remove_filter_state( # remove all states clear_filter_states(datasets) -\dontshow{if (requireNamespace("MultiAssayExperiment")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} - -# Requires MultiAssayExperiment from Bioconductor -data(miniACC, package = "MultiAssayExperiment") - -datasets <- init_filtered_data(list(mae = miniACC)) -fs <- teal_slices( - teal_slice( - dataname = "mae", varname = "years_to_birth", selected = c(30, 50), - keep_na = TRUE, keep_inf = FALSE - ), - teal_slice( - dataname = "mae", varname = "vital_status", selected = "1", - keep_na = FALSE - ), - teal_slice( - dataname = "mae", varname = "gender", selected = "female", - keep_na = TRUE - ), - teal_slice( - dataname = "mae", varname = "ARRAY_TYPE", selected = "", - keep_na = TRUE, experiment = "RPPAArray", arg = "subset" +\donttest{ +if (requireNamespace("MultiAssayExperiment", quietly = TRUE)) { + # Requires MultiAssayExperiment from Bioconductor + data(miniACC, package = "MultiAssayExperiment") + + datasets <- init_filtered_data(list(mae = miniACC)) + fs <- teal_slices( + teal_slice( + dataname = "mae", varname = "years_to_birth", selected = c(30, 50), + keep_na = TRUE, keep_inf = FALSE + ), + teal_slice( + dataname = "mae", varname = "vital_status", selected = "1", + keep_na = FALSE + ), + teal_slice( + dataname = "mae", varname = "gender", selected = "female", + keep_na = TRUE + ), + teal_slice( + dataname = "mae", varname = "ARRAY_TYPE", selected = "", + keep_na = TRUE, experiment = "RPPAArray", arg = "subset" + ) ) -) -# set initial filter state -set_filter_state(datasets, filter = fs) + # set initial filter state + set_filter_state(datasets, filter = fs) -# get filter state -get_filter_state(datasets) + # get filter state + get_filter_state(datasets) -# modify filter state -set_filter_state( - datasets, - teal_slices( - teal_slice(dataname = "mae", varname = "years_to_birth", selected = c(40, 60)) + # modify filter state + set_filter_state( + datasets, + teal_slices( + teal_slice(dataname = "mae", varname = "years_to_birth", selected = c(40, 60)) + ) ) -) -# remove specific filters -remove_filter_state( - datasets, - teal_slices( - teal_slice(dataname = "mae", varname = "years_to_birth"), - teal_slice(dataname = "mae", varname = "vital_status") + # remove specific filters + remove_filter_state( + datasets, + teal_slices( + teal_slice(dataname = "mae", varname = "years_to_birth"), + teal_slice(dataname = "mae", varname = "vital_status") + ) ) -) -# remove all states -clear_filter_states(datasets) -\dontshow{\}) # examplesIf} + # remove all states + clear_filter_states(datasets) +} +} } \seealso{ \code{\link{teal_slice}} diff --git a/man/init_filtered_dataset.Rd b/man/init_filtered_dataset.Rd index 473a7d4ff..7ef39b87d 100644 --- a/man/init_filtered_dataset.Rd +++ b/man/init_filtered_dataset.Rd @@ -76,31 +76,33 @@ if (interactive()) { shinyApp(ui, server) } -\dontshow{if (requireNamespace("MultiAssayExperiment")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -# MAEFilteredDataset example -library(shiny) +\donttest{ +if (requireNamespace("MultiAssayExperiment", quietly = TRUE)) { + # MAEFilteredDataset example + library(shiny) -data(miniACC, package = "MultiAssayExperiment") + data(miniACC, package = "MultiAssayExperiment") -MAE_fd <- init_filtered_dataset(miniACC, "MAE") -ui <- fluidPage( - MAE_fd$ui_add(id = "add"), - MAE_fd$ui_active("dataset"), - verbatimTextOutput("call") -) -server <- function(input, output, session) { - MAE_fd$srv_add(id = "add") - MAE_fd$srv_active(id = "dataset") - output$call <- renderText({ - paste( - vapply(MAE_fd$get_call(), deparse1, character(1), collapse = "\n"), - collapse = "\n" - ) - }) + MAE_fd <- init_filtered_dataset(miniACC, "MAE") + ui <- fluidPage( + MAE_fd$ui_add(id = "add"), + MAE_fd$ui_active("dataset"), + verbatimTextOutput("call") + ) + server <- function(input, output, session) { + MAE_fd$srv_add(id = "add") + MAE_fd$srv_active(id = "dataset") + output$call <- renderText({ + paste( + vapply(MAE_fd$get_call(), deparse1, character(1), collapse = "\n"), + collapse = "\n" + ) + }) + } + if (interactive()) { + shinyApp(ui, server) + } } -if (interactive()) { - shinyApp(ui, server) } -\dontshow{\}) # examplesIf} } \keyword{internal}