Merge pull request #259 from SafetyGraphics/dev-v0.11.0

dev-v0.11.0

.Rbuildignore

@@ -1,4 +1,4 @@
-^inst/eDISH_app/tests$
+^inst/safetyGraphics_app/tests$
 ^data-raw$
 ^.*\.Rproj$
 ^\.Rproj\.user$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: safetyGraphics
 Title: Create Interactive Graphics Related to Clinical Trial Safety
-Version: 0.10.1
+Version: 0.11.0
 Authors@R: c(
 	person("Jeremy", "Wildfire", email = "jeremy_wildfire@rhoworld.com", role = c("cre","aut")),
 	person("Becca", "Krouse", role="aut"),
@@ -37,5 +37,6 @@ Imports:
     tibble,
     utils,
     haven,
-    shinyWidgets
+    shinyWidgets,
+    tidyr
 VignetteBuilder: knitr

NAMESPACE

@@ -1,16 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
+export(chartRenderer)
 export(detectStandard)
-export(eDISH)
-export(eDISHOutput)
 export(generateSettings)
 export(getRequiredSettings)
 export(getSettingsMetadata)
-export(renderEDISH)
-export(renderSafetyHistogram)
+export(output_chartRenderer)
+export(render_chartRenderer)
 export(safetyGraphicsApp)
-export(safetyHistogram)
-export(safetyHistogramOutput)
+export(trimSettings)
 export(validateSettings)
 import(DT)
 import(dplyr)
@@ -35,4 +33,5 @@ importFrom(stringr,str_detect)
 importFrom(stringr,str_split)
 importFrom(stringr,str_subset)
 importFrom(tibble,tibble)
+importFrom(tidyr,gather)
 importFrom(utils,globalVariables)

R/chartRenderer.R

@@ -0,0 +1,144 @@
+#' Create an interactive graphics widget
+#'
+#' This function creates an nice interactive widget. See this vingette for more details regarding how to customize charts.
+#'
+#' @param data A data frame containing the labs data. Data must be structured as one record per study participant per time point per lab measure.
+#' @param debug_js print settings in javascript before rendering chart. Default: \code{FALSE}.
+#' @param settings Optional list of settings arguments to be converted to JSON using \code{jsonlite::toJSON(settings, auto_unbox = TRUE, dataframe = "rows", null = "null")}. Default: \code{NULL}.
+#' @param chart name of the chart to render
+#'
+#' @examples
+#' \dontrun{
+#'
+#' ## Create Histogram figure using a premade settings list
+#' details_list <- list(
+#'   list(value_col = "TRTP", label = "Treatment"),
+#'   list(value_col = "SEX", label = "Sex"),
+#'   list(value_col = "AGEGR1", label = "Age group")
+#' )
+#'
+#'
+#' filters_list <- list(
+#'   list(value_col = "TRTA", label = "Treatment"),
+#'   list(value_col = "SEX", label = "Sex"),
+#'   list(value_col = "RACE", label = "RACE"),
+#'   list(value_col = "AGEGR1", label = "Age group")
+#' )
+#'
+#' settingsl <- list(id_col = "USUBJID",
+#'       value_col = "AVAL",
+#'       measure_col = "PARAM",
+#'       unit_col = "PARAMCD",
+#'       normal_col_low = "A1LO",
+#'       normal_col_high = "A1HI",
+#'       details = details_list,
+#'       filters = filters_list)
+#'
+#' chartRenderer(data=adlbc, settings = settingsl, chart=safetyhistogram)
+#'
+#' }
+#'
+#' @import htmlwidgets
+#'
+#' @export
+chartRenderer <- function(data, debug_js = FALSE, settings = NULL, chart=NULL) {
+  # Chart specific customizastions (to be removed after js updates)
+  if(chart %in% c("paneledoutlierexplorer","safetyoutlierexplorer")){
+    settings$time_cols <- list(list(),list());
+    settings$time_cols[[1]]<-list(
+      type= "ordinal",
+      value_col= settings[["visit_col"]],
+      label= "Visit",
+      order_col= settings[["visitn_col"]],
+      order= NULL,
+      rotate_tick_labels= TRUE,
+      vertical_space= 100
+    )
+    settings$time_cols[[2]]<-list(
+      type= "linear",
+      value_col= settings[["studyday_col"]],
+      label= "Study Day",
+      order_col= settings[["studyday_col"]],
+      order= NULL,
+      rotate_tick_labels= FALSE,
+      vertical_space= 0
+    )
+  }
+
+  if(chart=="paneledoutlierexplorer"){
+    settings$lln_col <- settings[["normal_col_low"]]
+    settings$uln_col <- settings[["normal_col_high"]]
+  }
+
+  if(chart=="safetyshiftplot"){
+    settings$time_col<-settings[["visit_col"]]
+  }
+
+  if(chart=="safetyresultsovertime"){
+    settings$time_settings=list(
+      value_col= settings[["visit_col"]],
+      label= "Visit",
+      order_col= settings[["visitn_col"]],
+      order= NULL,
+      rotate_tick_labels= TRUE,
+      vertical_space= 100
+    )
+
+    settings$groups = settings$group_cols
+  }
+
+  #Set Chart Width
+  chartMaxWidth<-  safetyGraphics::chartsMetadata %>% filter(.data$chart==!!chart) %>% pull(.data$maxWidth)
+  settings$max_width <- chartMaxWidth
+
+  #Renderer
+  chartFunction<- safetyGraphics::chartsMetadata %>% filter(.data$chart==!!chart) %>% pull(.data$main)
+  rSettings = list(
+    data = data,
+    debug_js=debug_js,
+    chartFunction = chartFunction,
+    settings = jsonlite::toJSON(
+      settings,
+      auto_unbox = TRUE,
+      null = "null"
+    )
+  )
+
+  # create widget
+  htmlwidgets::createWidget(
+    name = 'chartRenderer',
+    rSettings,
+    # width = width,
+    # height = height,
+    package = 'safetyGraphics',
+    sizingPolicy = htmlwidgets::sizingPolicy(viewer.suppress=TRUE, browser.external = TRUE)
+  )
+}
+
+#' Shiny bindings for chartRenderer
+#'
+#' Output and render functions for using safetyhistogram within Shiny
+#' applications and interactive Rmd documents.
+#'
+#' @param outputId output variable to read from
+#' @param width,height Must be a valid CSS unit (like \code{'100\%'},
+#'   \code{'400px'}, \code{'auto'}) or a number, which will be coerced to a
+#'   string and have \code{'px'} appended.
+#' @param expr An expression that generates a chart
+#' @param env The environment in which to evaluate \code{expr}.
+#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
+#'   is useful if you want to save an expression in a variable.
+#'
+#' @name chartRenderer-shiny
+#'
+#' @export
+output_chartRenderer <- function(outputId, width = '100%', height = '400px'){
+  htmlwidgets::shinyWidgetOutput(outputId, 'chartRenderer', width, height, package = 'safetyGraphics')
+}
+
+#' @rdname chartRenderer-shiny
+#' @export
+render_chartRenderer <- function(expr, env = parent.frame(), quoted = FALSE) {
+  if (!quoted) { expr <- substitute(expr) } # force quoted
+  htmlwidgets::shinyRenderWidget(expr, output_chartRenderer, env, quoted = TRUE)
+}

R/chartsMetadata.R

@@ -0,0 +1,18 @@
+#' Charts Metadata
+#'
+#' Metadata about the charts available in the shiny app
+#'
+#' @format A data frame with 29 rows and 7 columns
+#' \describe{
+#'    \item{chart}{Name of the chart - one word, all lower case}
+#'    \item{label}{Nicely formatted name of the chart}
+#'    \item{description}{Description of the chart}
+#'    \item{repo_url}{Homepage for chart's code repository (if any)}
+#'    \item{settings_url}{Homepage for chart's settings documentation}
+#'    \item{main}{Name of the main function used to initialize the app. The function must accept "location" and "settings" parameters (in that order) and have an .init() method, expecting a json data array.}
+#'    \item{type}{type of chart (e.g. 'htmlwidget')}
+#'    \item{maxWidth}{max width for the widget in pixels}
+#' }
+#'
+#' @source Created for this package
+"chartsMetadata"