Merges default app options with the changes made in the UI
Usage
NCA_Server(
id,
FM_yaml_file = system.file(package = "formods", "templates", "formods.yaml"),
MOD_yaml_file = system.file(package = "ruminate", "templates", "NCA.yaml"),
id_ASM = "ASM",
id_UD = "UD",
id_DW = "DW",
deployed = FALSE,
react_state = NULL
)Arguments
- id
An ID string that corresponds with the ID used to call the modules UI elements
- FM_yaml_file
App configuration file with FM as main section.
- MOD_yaml_file
Module configuration file with MC as main section.
- id_ASM
ID string for the app state management module used to save and load app states
- id_UD
ID string for the upload data module used to save and load app states
- id_DW
ID string for the data wrangling module used to save and load app states
- deployed
Boolean variable indicating whether the app is deployed or not.
- react_state
Variable passed to server to allow reaction outside of module (
NULL)
Value
list containing the current state of the app including default values from the yaml file as well as any changes made by the user. The list has the following structure:
yaml: Full contents of the supplied yaml file.
MC: Module components of the yaml file.
NCA:
isgood: Boolean object indicating if the file was successfully loaded.
checksum: This is an MD5 sum of the contents element and can be used to detect changes in the state.
MOD_TYPE: Character data containing the type of module
"NCA"id: Character data containing the module id module in the session variable.
FM_yaml_file: App configuration file with FM as main section.
MOD_yaml_file: Module configuration file with MC as main section.
Examples
if(interactive()){
# original file: inst/templates/ruminate.R
library(formods)
library(ruminate)
# These are suggested packages
library(shinydashboard)
#library(ggpubr)
#library(plotly)
#library(shinybusy)
library(prompter)
#library(utils)
tags$style("@import url(https://use.fontawesome.com/releases/v6.4.0/css/all.css);")
# You can copy these locally and customize them for your own needs. Simply
# change the assignment to the local copy you've modified.
formods.yaml = system.file(package="formods", "templates", "formods.yaml")
ASM.yaml = system.file(package="formods", "templates", "ASM.yaml")
UD.yaml = system.file(package="formods", "templates", "UD.yaml")
DW.yaml = system.file(package="formods", "templates", "DW.yaml")
FG.yaml = system.file(package="formods", "templates", "FG.yaml")
NCA.yaml = system.file(package="ruminate", "templates", "NCA.yaml")
# Name of file to indicate we need to load testing data
ftmptest = file.path(tempdir(), "ruminate.test")
# Making sure that the deployed object is created
if(!exists("deployed")){
deployed = FALSE
}
# Making sure that the run_dev object is created
if(file.exists(file.path(tempdir(), "RUMINTE_DEVELOPMENT"))){
run_dev = TRUE
}else{
run_dev = FALSE
}
# If the SETUP.R file exists we source it
if(file.exists("SETUP.R")){
source("SETUP.R")
}
# If the DEPLOYED file marker existrs we set deployed to TRUE
if(file.exists("DEPLOYED")){
deployed = TRUE
}
CSS <- "
.wrapfig {
float: right;
shape-margin: 20px;
margin-right: 20px;
margin-bottom: 20px;
}
"
#https://fontawesome.com/icons?from=io
logo_url =
"https://raw.githubusercontent.com/john-harrold/ruminate/main/man/figures/logo.png"
data_url =
"https://github.com/john-harrold/formods/raw/master/inst/test_data/TEST_DATA.xlsx"
run_url =
"https://runruminate.ubiquity.tools/"
use_url =
"https://useruminate.ubiquity.tools/"
main_url =
"https://ruminate.ubiquity.tools/"
issue_url =
"https://github.com/john-harrold/ruminate/issues"
intro_text = tags$p(
"Ruminate is a shiny module for pharmacometric data processing,
visualization, and analysis. It consists of separate shiny modules that
provide interfaces into common R packages and provides the underlying code.
This is done to facilitate usage of those packages and to provide reproducible
analyses." ,
tags$li( "To find out more visit ",
tags$a("ruminate.ubiquity.tools", href=main_url),""),
tags$li( "To give it a try you can download a test dataset ",
tags$a("here", href=data_url),""),
tags$li( "Go to ",
tags$a("useruminate.ubiquity.tools", href=use_url)," for a video
demonstrating how to use ruminate"),
tags$li( "If you run into any problems, have questions, or want a feature please
visit the ",
tags$a("issues", href=issue_url)," page")
)
ui <- shinydashboard::dashboardPage(
skin="black",
shinydashboard::dashboardHeader(title="ruminate"),
shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(
shinydashboard::menuItem("Load/Save",
tabName="loadsave",
icon=icon("arrow-down-up-across-line")) ,
shinydashboard::menuItem("Transform Data", tabName="wrangle", icon=icon("shuffle")),
shinydashboard::menuItem("Visualize", tabName="plot", icon=icon("chart-line")),
shinydashboard::menuItem("NCA", tabName="nca", icon=icon("chart-area")),
shinydashboard::menuItem("App Info", tabName="sysinfo", icon=icon("book-medical"))
)
),
shinydashboard::dashboardBody(
tags$head(
tags$style(HTML(CSS))
),
shinydashboard::tabItems(
shinydashboard::tabItem(tabName="nca",
shinydashboard::box(title="Non-Compartmental Analysis", width=12,
fluidRow( prompter::use_prompt(),
column(width=12,
htmlOutput(NS("NCA", "NCA_ui_compact")))))
),
shinydashboard::tabItem(tabName="loadsave",
# shinydashboard::box(title=NULL, width=12,
shinydashboard::tabBox(
width = 12,
title = NULL,
shiny::tabPanel(id="load_data",
title=tagList(shiny::icon("file-arrow-up"),
"Load Data"),
fluidRow(
column(width=6,
div(style="display:inline-block;width:100%",
htmlOutput(NS("UD", "ui_ud_load_data"))),
htmlOutput(NS("UD", "ui_ud_clean")),
htmlOutput(NS("UD", "ui_ud_select_sheets")),
htmlOutput(NS("UD", "ui_ud_text_load_result"))),
column(width=6,
tags$p(
tags$img(
class = "wrapfig",
src = logo_url,
width = 150,
alt = "formods logo" ),
intro_text
))
),
fluidRow(
column(width=12,
div(style="display:inline-block;vertical-align:top",
htmlOutput(NS("UD", "ui_ud_data_preview")))
))
),
shiny::tabPanel(id="save_state",
title=tagList(shiny::icon("arrow-down-up-across-line"),
"Save or Load Analysis"),
fluidRow(
column(width=5,
div(style="display:inline-block;vertical-align:top",
htmlOutput(NS("ASM", "ui_asm_compact"))
))
)
)
)
# ),
),
shinydashboard::tabItem(tabName="wrangle",
shinydashboard::box(title="Transform and Create Views of Your Data", width=12,
fluidRow(
column(width=12,
htmlOutput(NS("DW", "DW_ui_compact")))))
),
shinydashboard::tabItem(tabName="plot",
shinydashboard::box(title="Visualize Data", width=12,
htmlOutput(NS("FG", "FG_ui_compact")))),
shinydashboard::tabItem(tabName="sysinfo",
# box(title="System Details", width=12,
shinydashboard::tabBox(
width = 12,
title = NULL,
shiny::tabPanel(id="sys_packages",
title=tagList(shiny::icon("box-open"),
"Installed Packages"),
htmlOutput(NS("ASM", "ui_asm_sys_packages"))
),
shiny::tabPanel(id="sys_modules",
title=tagList(shiny::icon("cubes"),
"Loaded Modules"),
htmlOutput(NS("ASM", "ui_asm_sys_modules"))
),
shiny::tabPanel(id="sys_log",
title=tagList(shiny::icon("clipboard-list"),
"Log"),
verbatimTextOutput(NS("ASM", "ui_asm_sys_log"))
),
shiny::tabPanel(id="sys_options",
title=tagList(shiny::icon("sliders"),
"R Options"),
htmlOutput(NS("ASM", "ui_asm_sys_options"))
)
# )
))
)
)
)
# Main app server
server <- function(input, output, session) {
# Empty reactive object to track and react to
# changes in the module state outside of the module
react_FM = reactiveValues()
# Module IDs and the order they are needed for code generation
mod_ids = c("UD", "DW", "FG", "NCA", "MB")
# If the ftmptest file is present we load test data
if(file.exists(ftmptest)){
sources = c(system.file(package="formods", "preload", "ASM_preload.yaml"),
system.file(package="formods", "preload", "UD_preload.yaml"),
system.file(package="formods", "preload", "FG_preload.yaml"),
system.file(package="formods", "preload", "DW_preload.yaml"),
system.file(package="ruminate", "preload", "NCA_preload.yaml"))
res = FM_app_preload(session=session, sources=sources)
}
# Module servers
formods::ASM_Server( id="ASM",
deployed = deployed,
react_state = react_FM,
FM_yaml_file = formods.yaml,
MOD_yaml_file = ASM.yaml,
mod_ids = mod_ids)
formods::UD_Server( id ="UD", id_ASM = "ASM",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = UD.yaml,
FM_yaml_file = formods.yaml)
formods::DW_Server( id="DW", id_ASM = "ASM",
id_UD = "UD",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = DW.yaml,
FM_yaml_file = formods.yaml)
formods::FG_Server( id="FG", id_ASM = "ASM",
id_UD = "UD", id_DW = "DW",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = FG.yaml,
FM_yaml_file = formods.yaml)
ruminate::NCA_Server(id ="NCA", id_ASM = "ASM",
id_UD = "UD", id_DW = "DW",
deployed = deployed,
react_state = react_FM,
MOD_yaml_file = NCA.yaml,
FM_yaml_file = formods.yaml)
}
shinyApp(ui, server)
}