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* create location for static R graphic code * update metadata to include static plot demo * if type=="static" create a static plot * pass chart type to chart module * shiny output binding depends on chart type * replace hardcode w/ generalized code * add overall loading indicator #286 * add workflows back in... * add hepexplorer implementations * incorporate plotly charts * add package to app * add prototype shiny module as custom chart * add type=="module" * meant to delete this * tweak inst/ folder structure for custom code * user settings #73 * add documentation for settingsLocation param * add pkgdown website * place custom charts in "examples" folder * remove example charts from metadata * update dependencies * move createChart to its own file * add hep explorer ggplot as an included chart * do not load plotly by default * move createChart to its own file * add hepexplorer_ggplot as included chart * add new chart to settingsMetadata docs * functionalize report RMD #312 * update safety-histogram to fix #355 * include Jeremys updates to safety histogram js * removing static hep explorer from included charts * update with beccas suggestions * make ggpot2 a suggested dependency * move button to bottom left and show after 3 seconds * adds addChart() function. * tweak documentation * add support for custom script in safetyGraphicsApp * refactor to support addChart() * minor tweaks * more functions for easy metadata manipulation * add default for charts * fixes minor issues from code review. * fix option logic. Clear tests. * clear checks * add text_key to settings description on hover * update renderers * update workflow link * add vignette and rebuild pkgdown * change hex to camel case * tweak customization workflow * update docs * update R script to camelCase * add delta-delta renderer. fix #380 * delete stray file. close #372 * tweak links. rebuild pkgdown site * update vignette * fix #383 and add option to pre-load custom datafiles * accomodate custom datafiles in UI * update safetyGraphicsApp params * clean stray old code * clear settings when ititializing app. fix #388. * fix typo in fix #388 * update hep-explorer renderer * update hep-explorer renderer * add pALT setting. * fix tests * update vignette. rebuild docs * update title * remove metadata from pre-loaded data * handle case where settingsLocation=NULL * update docs * spelling fixes * update vignette * remove old vignette Co-authored-by: Becca Krouse <rebecca_krouse@rhoworld.com> Co-authored-by: jwildfire <jwildfire@rhoworld.com>
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@@ -6,3 +6,9 @@ | |
| ^packrat/ | ||
| ^\.Rprofile$ | ||
| ^cran-comments.md$ | ||
| ^docs$ | ||
| ^_pkgdown.yml$ | ||
| ^Meta$ | ||
| ^_pkgdown\.yml$ | ||
| ^pkgdown$ | ||
| ^doc$ | ||
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@@ -41,4 +41,7 @@ packrat/lib*/ | |
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| #Local shinyTest folders | ||
| inst/eDISH_app/tests/*-current/ | ||
| customSettings/ | ||
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| doc | ||
| Meta | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,96 @@ | ||
| #' Adds a new chart for use in the safetyGraphics shiny app | ||
| #' | ||
| #' This function updates settings objects to add a new chart to the safetyGraphics shiny app | ||
| #' | ||
| #' This function makes it easy for users to add a new chart to the safetyGraphics shiny app, by making updates to the underlying metadata used by the package. Specifically, the function adds a row to chartsMetadata.rda describing the chart and adds a column to settingsMetadata.rda specifying which settings are used with the chart. If new settings are needed for the chart, the user should call addSetting() for each new setting required. | ||
| #' | ||
| #' @param chart Name of the chart - one word, all lower case | ||
| #' @param label Nicely formatted name of the chart | ||
| #' @param description Description of the chart | ||
| #' @param repo_url Homepage for chart's code repository (if any) | ||
| #' @param settings_url Homepage for chart's settings documentation | ||
| #' @param main Name of the main function used to initialize the app. If the type is htmlwidgets, the js function must accept "location" and "settings" parameters (in that order) and have an .init() method, expecting a json data array. Otherwise, the r function should accept named data and settings parameters, and should be loaded in the user's namespace. | ||
| #' @param type type of chart. Should be 'static', 'plotly' or 'module' | ||
| #' @param maxWidth max width for the widget in pixels | ||
| #' @param requiredSettings array of text_key values (matching those used in settingsMetadata) for the required settings for this chart | ||
| #' @param settingsLocation path where the custom settings will be loaded/saved. If metadata is not found in that location, it will be read from the package (e.g. safetyGraphics::settingsMetadata), and then written to the specified location once the new chart has been added. | ||
| #' @param overwrite overwrite any existing chart metadata? Note that having multiple charts with the same name is not supported and will cause unexpected results. default = true | ||
| #' | ||
| #' @importFrom rlang ":=" | ||
| #' @import dplyr | ||
| #' | ||
| #' @export | ||
| #' | ||
| addChart <- function( | ||
| chart, | ||
| label="", | ||
| description="", | ||
| repo_url="", | ||
| settings_url="", | ||
| main="character", | ||
| type='static', | ||
| maxWidth=1000, | ||
| requiredSettings=c(""), | ||
| settingsLocation=getwd(), | ||
| overwrite = TRUE | ||
| ){ | ||
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| # check inputs | ||
| stopifnot( | ||
| typeof(chart)=="character", | ||
| typeof(label)=="character", | ||
| typeof(description)=="character", | ||
| typeof(repo_url)=="character", | ||
| typeof(settings_url)=="character", | ||
| typeof(main)=="character", | ||
| typeof(type)=="character", | ||
| type %in% c("htmlwidget","plotly","static","module"), | ||
| is.numeric(maxWidth) | ||
| ) | ||
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| if(nchar(label)==0){ | ||
| label = chart | ||
| } | ||
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| # create settings for new chart | ||
| newChart <- list( | ||
| chart=chart, | ||
| main=main, | ||
| label=label, | ||
| description=description, | ||
| repo_url=repo_url, | ||
| settings_url=settings_url, | ||
| type=type, | ||
| maxWidth=maxWidth | ||
| ) | ||
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| # load charts metadata | ||
| chartsMetaPath <- paste(settingsLocation,"chartsMetadata.Rds",sep="/") | ||
| if(file.exists(chartsMetaPath)){ | ||
| chartsMeta <- readRDS(chartsMetaPath) | ||
| }else{ | ||
| chartsMeta <- safetyGraphics::chartsMetadata | ||
| } | ||
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| #delete rows for the specified chart if overwrite is true | ||
| if(overwrite){ | ||
| chartsMeta <- chartsMeta %>% filter(.data$chart != !!chart) | ||
| } | ||
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| # add custom chart settings and save | ||
| chartsMeta[nrow(chartsMeta)+1,] <- newChart | ||
| saveRDS(chartsMeta, chartsMetaPath) | ||
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| # add a column for the new chart to the settings metadata | ||
| settingsMetaPath <- paste(settingsLocation,"settingsMetadata.Rds",sep="/") | ||
| if(file.exists(settingsMetaPath)){ | ||
| settingsMeta <- readRDS(settingsMetaPath) | ||
| }else{ | ||
| settingsMeta <- safetyGraphics::settingsMetadata | ||
| } | ||
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| #Fill in the column based on requiredSettings and save | ||
| chart_col <- sym(paste0("chart_",chart)) | ||
| settingsMeta <- settingsMeta %>% mutate(!!chart_col := .data$text_key %in% !!requiredSettings) | ||
| saveRDS(settingsMeta, settingsMetaPath) | ||
| } |
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| @@ -0,0 +1,98 @@ | ||
| #' Adds a new setting for use in the safetyGraphics shiny app | ||
| #' | ||
| #' This function updates settings objects to add a new setting parameter to the safetyGraphics shiny app | ||
| #' | ||
| #' This function makes it easy for users to adds a new settings to the safetyGraphics shiny app by making updates to the underlying metadata used by the package. Specifically, the function adds a row to settingsMetadata.rda describing the setting. | ||
| #' | ||
| #' @param text_key Text key indicating the setting name. \code{'--'} delimiter indicates a nested setting | ||
| #' @param label Label | ||
| #' @param description Description | ||
| #' @param setting_type Expected type for setting value. Should be "character", "vector", "numeric" or "logical" | ||
| #' @param setting_required Flag indicating if the setting is required | ||
| #' @param column_mapping Flag indicating if the setting corresponds to a column in the associated data | ||
| #' @param column_type Expected type for the data column values. Should be "character","logical" or "numeric" | ||
| #' @param field_mapping Flag indicating whether the setting corresponds to a field-level mapping in the data | ||
| #' @param field_column_key Key for the column that provides options for the field-level mapping in the data | ||
| #' @param setting_cat Setting category (data, measure, appearance) | ||
| #' @param default Default value for non-data settings | ||
| #' @param charts character vector of charts using this setting | ||
| #' @param settingsLocation path where the custom settings will be loaded/saved. If metadata is not found in that location, it will be read from the package (e.g. safetyGraphics::settingsMetadata), and then written to the specified location once the new setting has been added. | ||
| #' @param overwrite overwrite any existing setting metadata? Note that having settings with the same name is not supported and will cause unexpected results. default = true | ||
| #' | ||
| #' @export | ||
| #' | ||
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| addSetting<-function( | ||
| text_key, | ||
| label, | ||
| description, | ||
| setting_type, | ||
| setting_required=FALSE, | ||
| column_mapping=FALSE, | ||
| column_type=NA, | ||
| field_mapping=FALSE, | ||
| field_column_key='', | ||
| setting_cat, | ||
| default='', | ||
| charts=c(), | ||
| settingsLocation=getwd(), | ||
| overwrite=TRUE | ||
| ){ | ||
|
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| # check inputs | ||
| stopifnot( | ||
| typeof(text_key)=="character", | ||
| typeof(label)=="character", | ||
| typeof(description)=="character", | ||
| typeof(setting_type)=="character", | ||
| setting_type %in% c("character","numeric","logical"), | ||
| typeof(setting_required)=="logical", | ||
| typeof(column_mapping)=="logical", | ||
| typeof(field_mapping)=="logical", | ||
| typeof(setting_cat)=="character" | ||
| ) | ||
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| if(nchar(label)==0){ | ||
| label = text_key | ||
| } | ||
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| # create object for new setting | ||
| newSetting <- list( | ||
| text_key=text_key, | ||
| label=label, | ||
| description=description, | ||
| setting_type=setting_type, | ||
| setting_required=setting_required, | ||
| column_mapping=column_mapping, | ||
| column_type=column_type, | ||
| field_mapping=field_mapping, | ||
| field_column_key=field_column_key, | ||
| setting_cat=setting_cat, | ||
| default=default | ||
| ) | ||
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| # load settings metadata | ||
| settingsMetaPath <- paste(settingsLocation,"settingsMetadata.Rds",sep="/") | ||
| if(file.exists(settingsMetaPath)){ | ||
| settingsMeta <- readRDS(settingsMetaPath) | ||
| }else{ | ||
| settingsMeta <- safetyGraphics::settingsMetadata | ||
| } | ||
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| # set chart flags for new setting | ||
| chartVars <- names(settingsMeta)[substr(names(settingsMeta),0,6)=="chart_"] | ||
| settingCharts <- paste0("chart_",charts) | ||
| for(varName in chartVars){ | ||
| newSetting[varName] <- varName %in% settingCharts | ||
| } | ||
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| #delete row for the specified chart if overwrite is true | ||
| if(overwrite){ | ||
| settingsMeta <- settingsMeta %>% filter(.data$text_key != !!text_key) | ||
| } | ||
|
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| # add custom chart settings and save | ||
| settingsMeta[nrow(settingsMeta)+1,] <- newSetting | ||
| saveRDS(settingsMeta, settingsMetaPath) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| #' Create a custom static or plotly R graphic | ||
| #' | ||
| #' @param type Type of chart. Options are \code{"static"} or \code{plotly}. | ||
| #' @param rSettings List containing all arguments needed for chart creation: | ||
| #' \code{rSettings = list( | ||
| #' data = data, | ||
| #' debug_js=debug_js, | ||
| #' chartFunction = chartFunction, | ||
| #' settings = jsonlite::toJSON( | ||
| #' settings, | ||
| #' auto_unbox = TRUE, | ||
| #' null = "null" | ||
| #' ))} | ||
| #' | ||
| #' @keywords internal | ||
| createChart <- function(type, rSettings){ | ||
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| data <- rSettings[["data"]] | ||
| settings <- jsonlite::fromJSON(rSettings[["settings"]]) | ||
| chartFunction <- rSettings[["chartFunction"]] | ||
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| #chartCode <- system.file("custom", type, paste0(chartFunction, ".R"), package = "safetyGraphics") | ||
| #source(chartCode) | ||
| chartFunction <- match.fun(chartFunction) | ||
| chartFunction(data, settings) | ||
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| } |
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