From 343b5f901f86079a77175ac5948196996c146719 Mon Sep 17 00:00:00 2001 From: m7pr Date: Fri, 4 Oct 2024 12:59:01 +0200 Subject: [PATCH 1/4] allow facet_var to be a delayed variables_choice for tm_g_gh_boxplot --- R/tm_g_gh_boxplot.R | 28 +++++++++++++--------------- R/utils-templ_ui.r | 13 +++++++++++++ 2 files changed, 26 insertions(+), 15 deletions(-) diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R index a8dc415a..f28c1743 100644 --- a/R/tm_g_gh_boxplot.R +++ b/R/tm_g_gh_boxplot.R @@ -207,7 +207,6 @@ tm_g_gh_boxplot <- function(label, dataname = dataname, param_var = param_var, trt_group = trt_group, - facet_var = facet_var, color_manual = color_manual, shape_manual = shape_manual, plot_height = plot_height, @@ -256,13 +255,6 @@ ui_g_boxplot <- function(id, ...) { multiple = FALSE ), uiOutput(ns("axis_selections")), - teal.widgets::optionalSelectInput( - ns("facet_var"), - label = "Facet by", - choices = get_choices(a$facet_var$choices), - selected = a$facet_var$selected, - multiple = FALSE - ), templ_ui_constraint(ns, label = "Data Constraint"), # required by constr_anl_q if (length(a$hline_vars) > 0) { teal.widgets::optionalSelectInput( @@ -312,7 +304,6 @@ srv_g_boxplot <- function(id, dataname, param_var, trt_group, - facet_var, color_manual, shape_manual, plot_height, @@ -331,6 +322,8 @@ srv_g_boxplot <- function(id, resolved_x <- teal.transform::resolve_delayed(module_args$xaxis_var, env) resolved_y <- teal.transform::resolve_delayed(module_args$yaxis_var, env) resolved_param <- teal.transform::resolve_delayed(module_args$param, env) + resolved_facet_var <- teal.transform::resolve_delayed(module_args$facet_var, env) + templ_ui_params_vars( session$ns, xparam_choices = resolved_param$choices, @@ -338,8 +331,12 @@ srv_g_boxplot <- function(id, xparam_label = module_args$"Select a Biomarker", xchoices = resolved_x$choices, xselected = resolved_x$selected, + ychoices = resolved_y$choices, - yselected = resolved_y$selected + yselected = resolved_y$selected, + + facet_choices = resolved_facet_var$choices, + facet_selected = resolved_facet_var$selected ) }) # reused in all modules @@ -477,6 +474,7 @@ srv_g_boxplot <- function(id, xaxis_var <- input$yaxis_var # nolint font_size <- input$font_size trt_group <- input$trt_group + facet_var <- input$facet_var anl_q()$qenv %>% teal.code::eval_code( code = bquote({ @@ -486,7 +484,7 @@ srv_g_boxplot <- function(id, param_var = .(param_var), param = .(param), xaxis_var = .(xaxis_var), - facet_var = .(input$facet_var) + facet_var = .(facet_var) ) }) ) @@ -511,8 +509,8 @@ srv_g_boxplot <- function(id, numeric_cols <- setdiff(names(dplyr::select_if(tbl, is.numeric)), "n") DT::datatable(tbl, - rownames = FALSE, options = list(scrollX = TRUE), - callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';") + rownames = FALSE, options = list(scrollX = TRUE), + callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';") ) %>% DT::formatRound(numeric_cols, 4) }) @@ -581,8 +579,8 @@ srv_g_boxplot <- function(id, numeric_cols <- names(dplyr::select_if(df, is.numeric)) DT::datatable(df, - rownames = FALSE, options = list(scrollX = TRUE), - callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';") + rownames = FALSE, options = list(scrollX = TRUE), + callback = DT::JS("$.fn.dataTable.ext.errMode = 'none';") ) %>% DT::formatRound(numeric_cols, 4) }) diff --git a/R/utils-templ_ui.r b/R/utils-templ_ui.r index 6d3ca49a..a0897e99 100644 --- a/R/utils-templ_ui.r +++ b/R/utils-templ_ui.r @@ -27,6 +27,10 @@ templ_ui_params_vars <- function(ns, ychoices = NULL, yselected = NULL, yvar_label = NULL, # variable, e.g. AVAL + # facet_var + facet_choices = NULL, + facet_selected = NULL, + multiple = FALSE) { if (is.null(xparam_choices) && !is.null(xchoices) && !is.null(yparam_choices)) { # otherwise, xchoices will appear first without any biomarker to select and this looks odd in the UI @@ -69,6 +73,15 @@ templ_ui_params_vars <- function(ns, ychoices, yselected, multiple = multiple ) + }, + if (!is.null(facet_choices)) { + teal.widgets::optionalSelectInput( + ns("facet_var"), + label = "Facet by", + choices = facet_choices, + selected = facet_selected, + multiple = FALSE + ) } ) } From 773105d604c4e1555d8b96ef64a9a198d0cf7881 Mon Sep 17 00:00:00 2001 From: m7pr Date: Tue, 21 Jan 2025 09:28:56 +0100 Subject: [PATCH 2/4] introduce transformators parameter to modules --- R/tm_g_gh_boxplot.R | 7 +++++-- R/tm_g_gh_correlationplot.R | 7 +++++-- R/tm_g_gh_density_distribution_plot.R | 7 +++++-- R/tm_g_gh_lineplot.R | 5 ++++- R/tm_g_gh_scatterplot.R | 7 +++++-- R/tm_g_gh_spaghettiplot.R | 5 ++++- man/tm_g_gh_boxplot.Rd | 10 +++++++--- man/tm_g_gh_correlationplot.Rd | 10 +++++++--- man/tm_g_gh_density_distribution_plot.Rd | 10 +++++++--- man/tm_g_gh_lineplot.Rd | 10 +++++++--- man/tm_g_gh_scatterplot.Rd | 10 +++++++--- man/tm_g_gh_spaghettiplot.Rd | 10 +++++++--- 12 files changed, 70 insertions(+), 28 deletions(-) diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R index f6b2a647..7f28fad3 100644 --- a/R/tm_g_gh_boxplot.R +++ b/R/tm_g_gh_boxplot.R @@ -37,6 +37,7 @@ #' @param alpha numeric vector to define transparency of plotted points. #' #' @inheritParams teal.widgets::standard_layout +#' @inheritParams teal::module #' #' @author Jeff Tomlinson (tomlinsj) jeffrey.tomlinson@roche.com #' @author Balazs Toth (tothb2) toth.balazs@gene.com @@ -168,7 +169,8 @@ tm_g_gh_boxplot <- function(label, dot_size = c(2, 1, 12), alpha = c(0.8, 0.0, 1.0), pre_output = NULL, - post_output = NULL) { + post_output = NULL, + transformators = list()) { message("Initializing tm_g_gh_boxplot") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -212,7 +214,8 @@ tm_g_gh_boxplot <- function(label, module_args = args ), ui = ui_g_boxplot, - ui_args = args + ui_args = args, + transformators = transformators ) } diff --git a/R/tm_g_gh_correlationplot.R b/R/tm_g_gh_correlationplot.R index 92bf2f0a..64747c6c 100644 --- a/R/tm_g_gh_correlationplot.R +++ b/R/tm_g_gh_correlationplot.R @@ -3,6 +3,7 @@ #' @description Scatter Plot Teal Module For Biomarker Analysis #' #' @inheritParams teal.widgets::standard_layout +#' @inheritParams teal::module #' @param label menu item label of the module in the teal app. #' @param dataname analysis data passed to the data argument of \code{\link[teal]{init}}. E.g. `ADaM` structured #' laboratory data frame \code{ADLB}. @@ -220,7 +221,8 @@ tm_g_gh_correlationplot <- function(label, dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, - post_output = NULL) { + post_output = NULL, + transformators = list()) { message("Initializing tm_g_gh_correlationplot") checkmate::assert_class(xaxis_param, "choices_selected") checkmate::assert_class(yaxis_param, "choices_selected") @@ -264,7 +266,8 @@ tm_g_gh_correlationplot <- function(label, module_args = args ), ui = ui_g_correlationplot, - ui_args = args + ui_args = args, + transformators = transformators ) } diff --git a/R/tm_g_gh_density_distribution_plot.R b/R/tm_g_gh_density_distribution_plot.R index 9f5ed2db..b6ff73ba 100644 --- a/R/tm_g_gh_density_distribution_plot.R +++ b/R/tm_g_gh_density_distribution_plot.R @@ -23,6 +23,7 @@ #' #' @inheritParams teal.widgets::standard_layout #' @inheritParams tm_g_gh_scatterplot +#' @inheritParams teal::module #' #' #' @author Nick Paszty (npaszty) paszty.nicholas@gene.com @@ -129,7 +130,8 @@ tm_g_gh_density_distribution_plot <- function(label, # nolint comb_line = TRUE, rotate_xlab = FALSE, pre_output = NULL, - post_output = NULL) { + post_output = NULL, + transformators = list()) { message("Initializing tm_g_gh_density_distribution_plot") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -168,7 +170,8 @@ tm_g_gh_density_distribution_plot <- function(label, # nolint module_args = args ), ui = ui_g_density_distribution_plot, - ui_args = args + ui_args = args, + transformators = transformators ) } diff --git a/R/tm_g_gh_lineplot.R b/R/tm_g_gh_lineplot.R index 66e88793..61b9c20d 100644 --- a/R/tm_g_gh_lineplot.R +++ b/R/tm_g_gh_lineplot.R @@ -3,6 +3,7 @@ #' This teal module renders the UI and calls the function that creates a line plot. #' #' @inheritParams teal.widgets::standard_layout +#' @inheritParams teal::module #' @param label menu item label of the module in the teal app. #' @param dataname analysis data passed to the data argument of \code{\link[teal]{init}}. E.g. `ADaM` structured #' laboratory data frame `ADLB`. @@ -155,7 +156,8 @@ tm_g_gh_lineplot <- function(label, count_threshold = 0, table_font_size = c(12, 4, 20), dot_size = c(2, 1, 12), - plot_relative_height_value = 1000) { + plot_relative_height_value = 1000, + transformators = list()) { message("Initializing tm_g_gh_lineplot") # Validate string inputs checkmate::assert_string(label) @@ -220,6 +222,7 @@ tm_g_gh_lineplot <- function(label, ), ui = ui_lineplot, ui_args = args, + transformators = transformators, datanames = dataname ) } diff --git a/R/tm_g_gh_scatterplot.R b/R/tm_g_gh_scatterplot.R index b25283e3..37457793 100644 --- a/R/tm_g_gh_scatterplot.R +++ b/R/tm_g_gh_scatterplot.R @@ -7,6 +7,7 @@ #' instead. #' #' @inheritParams teal.widgets::standard_layout +#' @inheritParams teal::module #' @param label menu item label of the module in the teal app. #' @param dataname analysis data passed to the data argument of \code{\link[teal]{init}}. E.g. `ADaM` structured #' laboratory data frame \code{ADLB}. @@ -138,7 +139,8 @@ tm_g_gh_scatterplot <- function(label, dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, - post_output = NULL) { + post_output = NULL, + transformators = list()) { lifecycle::deprecate_soft( when = "0.1.15", what = "tm_g_gh_scatterplot()", @@ -178,7 +180,8 @@ tm_g_gh_scatterplot <- function(label, module_args = args ), ui = ui_g_scatterplot, - ui_args = args + ui_args = args, + transformators = transformators ) } diff --git a/R/tm_g_gh_spaghettiplot.R b/R/tm_g_gh_spaghettiplot.R index 1da56159..ca9566df 100644 --- a/R/tm_g_gh_spaghettiplot.R +++ b/R/tm_g_gh_spaghettiplot.R @@ -46,6 +46,7 @@ #' @param hline_vars_colors a character vector naming the colors for the additional horizontal lines. #' @param hline_vars_labels a character vector naming the labels for the additional horizontal lines that will appear #' in the legend. +#' @inheritParams teal::module #' @inheritParams teal.widgets::standard_layout #' #' @author Wenyi Liu (luiw2) wenyi.liu@roche.com @@ -188,7 +189,8 @@ tm_g_gh_spaghettiplot <- function(label, hline_vars_colors = "green", hline_vars_labels = hline_vars, pre_output = NULL, - post_output = NULL) { + post_output = NULL, + transformators = list()) { message("Initializing tm_g_gh_spaghettiplot") # Validate string inputs @@ -258,6 +260,7 @@ tm_g_gh_spaghettiplot <- function(label, ), ui = g_ui_spaghettiplot, ui_args = args, + transformators = transformators, datanames = dataname ) } diff --git a/man/tm_g_gh_boxplot.Rd b/man/tm_g_gh_boxplot.Rd index ee7ac16d..12d0e068 100644 --- a/man/tm_g_gh_boxplot.Rd +++ b/man/tm_g_gh_boxplot.Rd @@ -30,7 +30,8 @@ tm_g_gh_boxplot( dot_size = c(2, 1, 12), alpha = c(0.8, 0, 1), pre_output = NULL, - post_output = NULL + post_output = NULL, + transformators = list() ) } \arguments{ @@ -90,11 +91,14 @@ in the legend.} \item{alpha}{numeric vector to define transparency of plotted points.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} + +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} } \value{ an \code{\link[teal]{module}} object diff --git a/man/tm_g_gh_correlationplot.Rd b/man/tm_g_gh_correlationplot.Rd index bf8cc9ae..9e039460 100644 --- a/man/tm_g_gh_correlationplot.Rd +++ b/man/tm_g_gh_correlationplot.Rd @@ -39,7 +39,8 @@ tm_g_gh_correlationplot( dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, - post_output = NULL + post_output = NULL, + transformators = list() ) } \arguments{ @@ -116,11 +117,14 @@ naming the label for the arbitrary horizontal lines.} \item{reg_text_size}{font size control for regression line annotations.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} + +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} } \description{ Scatter Plot Teal Module For Biomarker Analysis diff --git a/man/tm_g_gh_density_distribution_plot.Rd b/man/tm_g_gh_density_distribution_plot.Rd index e567757a..cc16697e 100644 --- a/man/tm_g_gh_density_distribution_plot.Rd +++ b/man/tm_g_gh_density_distribution_plot.Rd @@ -24,7 +24,8 @@ tm_g_gh_density_distribution_plot( comb_line = TRUE, rotate_xlab = FALSE, pre_output = NULL, - post_output = NULL + post_output = NULL, + transformators = list() ) } \arguments{ @@ -68,11 +69,14 @@ naming the label for the arbitrary horizontal lines.} \item{rotate_xlab}{45 degree rotation of \code{x-axis} values.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} + +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} } \description{ This teal module renders the UI and calls the functions that create a density distribution plot diff --git a/man/tm_g_gh_lineplot.Rd b/man/tm_g_gh_lineplot.Rd index a748bbca..a2b6c6cd 100644 --- a/man/tm_g_gh_lineplot.Rd +++ b/man/tm_g_gh_lineplot.Rd @@ -36,7 +36,8 @@ tm_g_gh_lineplot( count_threshold = 0, table_font_size = c(12, 4, 20), dot_size = c(2, 1, 12), - plot_relative_height_value = 1000 + plot_relative_height_value = 1000, + transformators = list() ) } \arguments{ @@ -100,10 +101,10 @@ Default value is waive().} \item{dodge}{controls the position dodge of error bar} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{count_threshold}{minimum count of observations (as listed in the output table) to plot @@ -115,6 +116,9 @@ nodes on the graph} \item{plot_relative_height_value}{numeric value between 500 and 5000 for controlling the starting value of the relative plot height slider} + +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} } \value{ \code{shiny} object diff --git a/man/tm_g_gh_scatterplot.Rd b/man/tm_g_gh_scatterplot.Rd index e0587cbf..31568ba3 100644 --- a/man/tm_g_gh_scatterplot.Rd +++ b/man/tm_g_gh_scatterplot.Rd @@ -26,7 +26,8 @@ tm_g_gh_scatterplot( dot_size = c(1, 1, 12), reg_text_size = c(3, 3, 10), pre_output = NULL, - post_output = NULL + post_output = NULL, + transformators = list() ) } \arguments{ @@ -73,11 +74,14 @@ TRUE.} \item{reg_text_size}{font size control for regression line annotations.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} + +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} diff --git a/man/tm_g_gh_spaghettiplot.Rd b/man/tm_g_gh_spaghettiplot.Rd index df6779f0..b588f6c6 100644 --- a/man/tm_g_gh_spaghettiplot.Rd +++ b/man/tm_g_gh_spaghettiplot.Rd @@ -36,7 +36,8 @@ tm_g_gh_spaghettiplot( hline_vars_colors = "green", hline_vars_labels = hline_vars, pre_output = NULL, - post_output = NULL + post_output = NULL, + transformators = list() ) } \arguments{ @@ -113,11 +114,14 @@ naming the label for the arbitrary horizontal lines.} \item{hline_vars_labels}{a character vector naming the labels for the additional horizontal lines that will appear in the legend.} -\item{pre_output}{(\code{shiny.tag}, optional)\cr +\item{pre_output}{(\code{shiny.tag}) optional,\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} + +\item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. +To learn more check \code{vignette("data-transform-as-shiny-module", package = "teal")}.} } \value{ \code{shiny} object From 65bff681aeb4059326348770ba0a19e45c44f64e Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 21 Jan 2025 08:34:49 +0000 Subject: [PATCH 3/4] [skip style] [skip vbump] Restyle files --- R/tm_g_gh_boxplot.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R index 7f28fad3..7c17331c 100644 --- a/R/tm_g_gh_boxplot.R +++ b/R/tm_g_gh_boxplot.R @@ -322,10 +322,8 @@ srv_g_boxplot <- function(id, xparam_label = module_args$"Select a Biomarker", xchoices = resolved_x$choices, xselected = resolved_x$selected, - ychoices = resolved_y$choices, yselected = resolved_y$selected, - facet_choices = resolved_facet_var$choices, facet_selected = resolved_facet_var$selected, trt_choices = resolved_trt$choices, From e57e3a953b874abaa82b1565fe34dc97ed98cc41 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 21 Jan 2025 08:40:19 +0000 Subject: [PATCH 4/4] [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update --- man/tm_g_gh_boxplot.Rd | 4 ++-- man/tm_g_gh_correlationplot.Rd | 4 ++-- man/tm_g_gh_density_distribution_plot.Rd | 4 ++-- man/tm_g_gh_lineplot.Rd | 4 ++-- man/tm_g_gh_scatterplot.Rd | 4 ++-- man/tm_g_gh_spaghettiplot.Rd | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/man/tm_g_gh_boxplot.Rd b/man/tm_g_gh_boxplot.Rd index 12d0e068..01a20250 100644 --- a/man/tm_g_gh_boxplot.Rd +++ b/man/tm_g_gh_boxplot.Rd @@ -91,10 +91,10 @@ in the legend.} \item{alpha}{numeric vector to define transparency of plotted points.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. diff --git a/man/tm_g_gh_correlationplot.Rd b/man/tm_g_gh_correlationplot.Rd index 9e039460..77a4b933 100644 --- a/man/tm_g_gh_correlationplot.Rd +++ b/man/tm_g_gh_correlationplot.Rd @@ -117,10 +117,10 @@ naming the label for the arbitrary horizontal lines.} \item{reg_text_size}{font size control for regression line annotations.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. diff --git a/man/tm_g_gh_density_distribution_plot.Rd b/man/tm_g_gh_density_distribution_plot.Rd index cc16697e..a303e809 100644 --- a/man/tm_g_gh_density_distribution_plot.Rd +++ b/man/tm_g_gh_density_distribution_plot.Rd @@ -69,10 +69,10 @@ naming the label for the arbitrary horizontal lines.} \item{rotate_xlab}{45 degree rotation of \code{x-axis} values.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. diff --git a/man/tm_g_gh_lineplot.Rd b/man/tm_g_gh_lineplot.Rd index a2b6c6cd..82af5077 100644 --- a/man/tm_g_gh_lineplot.Rd +++ b/man/tm_g_gh_lineplot.Rd @@ -101,10 +101,10 @@ Default value is waive().} \item{dodge}{controls the position dodge of error bar} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{count_threshold}{minimum count of observations (as listed in the output table) to plot diff --git a/man/tm_g_gh_scatterplot.Rd b/man/tm_g_gh_scatterplot.Rd index 31568ba3..08073e75 100644 --- a/man/tm_g_gh_scatterplot.Rd +++ b/man/tm_g_gh_scatterplot.Rd @@ -74,10 +74,10 @@ TRUE.} \item{reg_text_size}{font size control for regression line annotations.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input. diff --git a/man/tm_g_gh_spaghettiplot.Rd b/man/tm_g_gh_spaghettiplot.Rd index b588f6c6..512baaaf 100644 --- a/man/tm_g_gh_spaghettiplot.Rd +++ b/man/tm_g_gh_spaghettiplot.Rd @@ -114,10 +114,10 @@ naming the label for the arbitrary horizontal lines.} \item{hline_vars_labels}{a character vector naming the labels for the additional horizontal lines that will appear in the legend.} -\item{pre_output}{(\code{shiny.tag}) optional,\cr +\item{pre_output}{(\code{shiny.tag}, optional)\cr with text placed before the output to put the output into context. For example a title.} -\item{post_output}{(\code{shiny.tag}) optional, with text placed after the output to put the output +\item{post_output}{(\code{shiny.tag}, optional) with text placed after the output to put the output into context. For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are useful.} \item{transformators}{(\code{list} of \code{teal_transform_module}) that will be applied to transform module's data input.