diff --git a/DESCRIPTION b/DESCRIPTION index 6707f9d6..3023082e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Type: Package Package: teal.goshawk Title: Longitudinal Visualization `teal` Modules -Version: 0.2.0.9021 -Date: 2025-01-15 +Version: 0.2.0.9022 +Date: 2025-01-21 Authors@R: c( person("Nick", "Paszty", , "nick.paszty@gene.com", role = c("aut", "cre")), person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index d957b4b4..4e21ce9d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# teal.goshawk 0.2.0.9021 +# teal.goshawk 0.2.0.9022 # teal.goshawk 0.2.0 diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R index 40a33a16..7c17331c 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 c9669c0a..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{ @@ -95,6 +96,9 @@ with text placed before the output to put the output into context. For example a \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 0890823f..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{ @@ -121,6 +122,9 @@ with text placed before the output to put the output into context. For example a \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 37520ad1..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{ @@ -73,6 +74,9 @@ with text placed before the output to put the output into context. For example a \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 99eae84b..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{ @@ -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 0875f92c..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{ @@ -78,6 +79,9 @@ with text placed before the output to put the output into context. For example a \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 ac816ff9..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{ @@ -118,6 +119,9 @@ with text placed before the output to put the output into context. For example a \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