inst/fishPBPK_pop/ui.R
In ScitoVation/plethem: Population Life Course Exposure to Health Effects Modeling
library(shiny)
library(shinyBS)
library(shinydashboard)
library(shinyWidgets)
library(V8)
library(ggplot2)
library(shinyjs)
jscode <- "
shinyjs.disableTab = function(name) {
var tab = $('#'+name);
tab.bind('click.tab', function(e) {
e.preventDefault();
return false;
});
tab.addClass('disabled-comp');
}
shinyjs.enableTab = function(name) {
var tab = $('#'+name);
tab.unbind('click.tab');
tab.removeClass('disabled-comp');
}
"
css <- "div .disabled-comp {
color: #aaa !important;
border-color: #a00 !important;
background-color: #a00 !important;
}"
################################exposure sidebar
expo_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="ms_expo_sidebar",
menuItem("Inspiration Through Gills", tabName = "ins",selected = T)
))
################################compartment sidebar
comp_sidebar <- shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(id="compsidebar",
# tags$div(shinyWidgets::radioGroupButtons("ms_org",
# label = "Select Organism",
# choices = c("Human" = "ha","Rat"="ra"),
# selected = "ha",size = "normal",
# checkIcon = list(yes = icon('ok',lib ="glyphicon")))),
menuItem("Physiological Parameters",
tabName = "physiolocal_parameters", selected = TRUE),
menuItem("Fat",tabName = "fat"),
menuItem("Liver",tabName = "liv"),
menuItem("Kidney",tabName = "kdn"),
menuItem("Poorly Perfused Tissue",tabName = "spf"),
menuItem("Richly Perfused Tissue",tabName = "rpf")
)
)
###############################Chemical Sidebar
chem_sidebar <- shinydashboard::dashboardSidebar()
###########################plots-Body
plot_body <- fluidPage(
tabItem(tabName = "plots",
fluidRow(
bsCollapse(id="plts", multiple = TRUE,
bsCollapsePanel(title = "Exposure Plots", style = "primary",
column(3,
wellPanel(
checkboxInput("ch_dose", "Instaneous Dose", value = TRUE, width = NULL),
checkboxInput("ch_totdose", "Total Dose", value = TRUE, width = NULL)
)
),
column(9,
tabBox(width=12, height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
column(4,offset = 4,
radioButtons("r_expo_type",label = "Select Exposure",inline = TRUE,
choices = c("Active"="act","All"="all"),
selected = "act"))
),
fluidRow(
plotly::plotlyOutput("exposureplt")
)
),
tabPanel("Table",
DT::DTOutput("expotble"),
downloadButton("expodwnld",label = "Get Data")))
)),
bsCollapsePanel(title = "Concentration Plots", style = "primary",
column(3,
tabsetPanel(
tabPanel("Model",value = "model",
shinyWidgets::multiInput("cplt_comp",label = tags$h4("Select Compartment"),
choices = list("Total Fat"="fat",
"Total Liver"="liv",
"Total Kidney"="kdn",
"Total Rapidly Perfused"="rpf",
"Total Slowly Perfused "="spf",
"Total Metabolite"="met"
)
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$h4("Select Datasets"),
choices = c("No Dataset"="none"),
selected = "none")
)
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_cplt_type",label = "Concentration Units",inline = TRUE,
choices = c("mg/L"="mgl","\u00B5Molar"="um"),
selected = "um")
)
),
fluidRow(
plotly::plotlyOutput("concplt")
)
),
tabPanel("Table",
DT::DTOutput("conctble"),
downloadButton("cdwnld",label ="Get Data"))
))),
bsCollapsePanel(title = "Mass Balance Plots", style = "primary",
column(8, offset = 2,
tabBox(width = 12, height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
plotOutput("balplt")
)
),
tabPanel("Table",
DT::DTOutput("baltble"),
downloadButton("cmbaldwnld",label ="Get Data"))
))
)
)
))
)
#####################compartment Body
comp_body <- dashboardBody(
tabItems(
tabItem(
tabName = "physiolocal_parameters",
fluidRow(
column(4,
selectInput("ms_org", label = "Organism",
choices = list("Trout" = "tr","Catfish"="cf"),
selected = "tr")
),
column(4,
numericInput("ms_bw","Body Weight (kg)",1,0.1,90,0.1)),
column(4,
numericInput("ms_qc","Cardiac Output (L/h)",2.06,1,50,0.1))
),
fluidRow(
column(4,
numericInput("ms_qg","Effective respiratory rate (L/h)",
min =0 , max =10, value =7.2)),
column(4,
numericInput("ms_pbldw", label = "Blood-Water Partition Coefficient",
value = 5.17, min = 0)
))),
tabItem(
tabName = "fat",
fluidRow(
column(6,
numericInput("ms_vfatc","Volume (L)",min =0, max = 1, value =0.098, step = 0.01)),
column(6,
numericInput("ms_qfatc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.085))
),
fluidRow(class="",
column(6,
numericInput("ms_pfat","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "liv",
fluidRow(
column(6,
numericInput("ms_vlivc","Volume (L)",min =0, max = 1, value =0.012, step = 0.01)),
column(6,
numericInput("ms_qlivc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1,
value =0.029))
),
fluidRow(class="",
column(6,
numericInput("ms_pliv","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "kdn",
fluidRow(
column(6,
numericInput("ms_vkdnc","Volume (L)",min =0, max = 1, value =0.009, step = 0.01)),
column(6,
numericInput("ms_qkdnc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.056))
),
fluidRow(class="",
column(6,
numericInput("ms_pkdn","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "rpf",
fluidRow(
column(6,
numericInput("ms_vrpfc","Volume (L)",min =0, max = 1, value =0.063, step = 0.01)),
column(6,
numericInput("ms_qrpfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.23))
),
fluidRow(class="",
column(6,
numericInput("ms_prpf","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "spf",
fluidRow(
column(4,
numericInput("ms_vspfc","Volume (L)",min =0, max = 1, value =0.818, step = 0.01)),
column(4,
numericInput("ms_qspfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.6))
),
fluidRow(class="",
column(6,
numericInput("ms_pspf","Partition Coefficient",1,0,2, 0.01)))
)
)
)
####################chemical Body
chem_body <- dashboardBody(
fluidPage(id="Chemicals",
tags$h4("Chemical Parameters", class="pager-header"),
fluidRow(
column(6,
numericInput("ms_mw","Molecular Weight (g/mol)",167.8,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_vmax",paste0("Maximum Metabolism Rate (mg/h) or Intrinsic Clearance (L/h)"),0,0,250,0.01)),
column(6,
numericInput("ms_km","Michaelis-Menten Constant for Metabolism (mg/L) or -1 if Using Intrinsic Clearance",0,0,250,0.01))
),
# fluidRow(
# column(6,
# numericInput("ms_intcl", "Intrinsic Clearance (L/h)", 0,250,0.01))
# ),
# fluidRow(
# column(6,
# checkboxInput("ms_useIntcl", paste0("","Use Intrinsic Clearance",sep="\n"), value = FALSE))
# )
))
######################exposure Body
expo_body <- dashboardBody(
tabItems(
tabItem(
tabName = "ins",
fluidRow(
column(4,
numericInput("ms_cins",label="Concentration in Water (mg/L)",
value =1.062,
step= 0.01)
)
)
)
)
)
#################Shiny UI
shinyUI(fluidPage(
shinyjs::useShinyjs(),
shinyWidgets::useSweetAlert(),
theme = shinythemes::shinytheme("spacelab"),
includeCSS("www/styles.css"),
shinyjs::extendShinyjs(text = jscode, functions = c("disableTab", "enableTab")),
shinyjs::inlineCSS(css),
titlePanel(title="", windowTitle = "PLETHEM rapidPBPK"),
tags$head(
tags$meta(charset="utf-8"),
tags$meta(name="viewport", content="width=device-width, initial-scale=1"),
tags$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
#rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,
tabPanel("",value = "Home",icon =icon("home"),
includeHTML("www/home.html")),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$h4("Overwrite existing Parameter Set ?")),
column(2,
bsButton("exposave_yes","Yes",block = TRUE))
)),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 9, offset = 0,
selectizeInput("sel_expo",NULL,
choices = NULL,
options= list(placeholder = "Exposure Parameter Set",
openOnFocus = T))),
column(width = 3, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_sverest_expo","btn_saveas_expo"),
c("Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
expo_sidebar,
expo_body
)
)
)
),
tabPanel("Chemical",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 7, offset = 0,
selectizeInput("sel_chem",NULL,
choices = NULL,
options= list(placeholder = "Chemicals",
openOnFocus = T))),
column(width = 5, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_chem","btn_sverest_chem","btn_saveas_chem"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
chem_sidebar,
chem_body
)
))
),
tabPanel("Physiological",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 9, offset = 0,
selectizeInput("sel_physio",NULL,
choices = NULL,
options= list(placeholder = "Physiological Parameter Set",
openOnFocus = T))),
column(width = 3, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_physio","btn_sverest_physio","btn_saveas_physio"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
comp_sidebar,
comp_body
)
)
)
),
tabPanel("Uncertanity and Variability",
dashboardPage(
dashboardHeader(disable = T),
dashboardSidebar(
shinydashboard::sidebarMenu(
menuItem("Physiological",
tabName = "var_physio"),
menuItem("Chemical",
tabName = "var_chem"),
menuItem("Exposure",
tabName = "var_expo")
)
),
dashboardBody(tabItems(
tabItem(tabName = "var_physio",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_physio_var",NULL,
choices = NULL,
options= list(placeholder = "Population Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varphys","btn_edit_varphys","btn_import_varphys"),
c("New","Edit","Import"),
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("physio_var_tble")
)
)
),
tabItem(tabName = "var_chem",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_chem_var",NULL,
choices = NULL,
options= list(placeholder = "Chemical Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varchem","btn_edit_varchem","btn_import_varchem"),
c("New","Edit","Import"),
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("chem_var_tble"))
)
),
tabItem(tabName = "var_expo",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_expo_var",NULL,
choices = NULL,
options= list(placeholder = "Exposure Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varexpo","btn_edit_varexpo","btn_import_varexpo"),
c("New","Edit","Import"),
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("expo_var_tble"))
)
)
)
)
)
),
tabPanel("Simulations",
fluidPage(
fluidRow(tags$h4("")),
fluidRow(
column(5,
shinyWidgets::dropdownButton(
tagList(
textInput("sim_name","Name"),
textAreaInput("sim_descrp","Description",rows = 2,resize = "none"),
fluidRow(
column(6,
selectizeInput("sel_set_chem","Select Chemical",choices = NULL)
),
column(6,
selectizeInput("sel_set_chemvar","Select Variability",choices = NULL)
)
),
fluidRow(
column(6,
selectizeInput("sel_set_expo","Select Exposure",choices = NULL)
),
column(6,
selectizeInput("sel_set_expovar","Select Variability",choices = NULL)
)
),
fluidRow(
column(6,
selectizeInput("sel_set_physio","Select Compartment",choices = NULL)
),
column(6,
selectizeInput("sel_set_physiovar","Select Variability",choices = NULL)
)
),
fluidRow(
column(4,
numericInput("sim_start","Simulation Start Time (h)",0)
),
column(4,
numericInput("sim_dur","Simulation Duration (h)",0)
),
column(4,
numericInput("mc_num","Number of Monte Carlo Runs",1000)
)
),
checkboxInput("mc_mode","Run Monte Carlo Simulation",T),
shinyWidgets::actionBttn("save_sim",NULL,
icon = icon("floppy-save",lib = "glyphicon"),
style = "material-circle")
),
icon = icon("plus"),circle = F,
tooltip = F,size = "default",right = F,
width = validateCssUnit("100%"),
label = "Create new simulation",
status = "default" )),
column(3,
shinyBS::bsButton("run_sim","Run Simulation",
style = "primary",block = TRUE))
),
fluidRow(
br(),
selectizeInput("sel_sim", "Select a Simulation",
choices =NULL, width = validateCssUnit("99%"))
),
fluidRow(
wellPanel(id= "Simulationdetails1",
fluidRow(
column(8,offset =2,
tags$h4("Simulation Description"),
textOutput("sim_descrp")
)
),
fluidRow(
column(6,
tags$h4("Simulation Start (h)"),
textOutput("sim_start")
),
column(6,
tags$h4("Simulation Duration (h)"),
textOutput("sim_dur")
)
),
fluidRow(
column(6,
tags$h4("Chemical Name"),
textOutput("sim_chem")
),
column(4,
tags$h4("Exposure Name"),
textOutput("sim_expo")
)
)#,
# fluidRow(
# column(4,
# tags$h4("Age"),
# textOutput("sim_age")
# ),
# column(4,
# tags$h4("Gender"),
# textOutput("sim_gender")
# )
# ),
# fluidRow(
# column(4,
# tags$h4("Metabolism Type"),
# textOutput("sim_metab_type")
# ),
# column(4,
# tags$h4("Value"),
# textOutput("sim_metab_val")
# ),
# column(4,
# tags$h4("Units"),
# textOutput("sim_metab_units")
# )
#
# )
)
)
))
)),
tabPanel("Model Output",icon = icon("line-chart"),value = "output",
fluidRow(
column(2,
bsButton("btnAddData","Add Dataset",block = TRUE,style = "primary")
),
column(3, offset= 6,
downloadButton("downloadModel", "Download Model",class = "btn btn-primary btn-block")
),
column(1,
shinyBS::bsButton("btnOutputIntro", "Need help?",block = TRUE,style = "info"))
),
tabsetPanel(id = "Modeloutput", type = "tabs",
tabPanel("Plots",
plot_body
),
tabPanel("Parameters",
fluidPage(
fluidRow(
box(title = "Exposure Parameters",width = 4,
DT::DTOutput("expo_params_tble")),
box(title = "Chemical Specific Parameters",width = 4,
DT::DTOutput("chem_params_tble")),
box(title = "Physiological Parameters",width = 4,
DT::DTOutput("physio_params_tble"))
),
fluidRow(
downloadButton("btn_param_dwnld",
label = "Download All Paramters")
))
)
)
),
tabPanel( id = "help" , title= "help", value = "Help", icon = icon("info")),
tabPanel(title = "Quit",value = "stop",icon=icon("power-off"))
)
))
ScitoVation/plethem documentation built on Oct. 1, 2020, 3:37 a.m.
R Package Documentation
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library(shiny)
library(shinyBS)
library(shinydashboard)
library(shinyWidgets)
library(V8)
library(ggplot2)
library(shinyjs)
jscode <- "
shinyjs.disableTab = function(name) {
var tab = $('#'+name);
tab.bind('click.tab', function(e) {
e.preventDefault();
return false;
});
tab.addClass('disabled-comp');
}
shinyjs.enableTab = function(name) {
var tab = $('#'+name);
tab.unbind('click.tab');
tab.removeClass('disabled-comp');
}
"
css <- "div .disabled-comp {
color: #aaa !important;
border-color: #a00 !important;
background-color: #a00 !important;
}"
################################exposure sidebar
expo_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="ms_expo_sidebar",
menuItem("Inspiration Through Gills", tabName = "ins",selected = T)
))
################################compartment sidebar
comp_sidebar <- shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(id="compsidebar",
# tags$div(shinyWidgets::radioGroupButtons("ms_org",
# label = "Select Organism",
# choices = c("Human" = "ha","Rat"="ra"),
# selected = "ha",size = "normal",
# checkIcon = list(yes = icon('ok',lib ="glyphicon")))),
menuItem("Physiological Parameters",
tabName = "physiolocal_parameters", selected = TRUE),
menuItem("Fat",tabName = "fat"),
menuItem("Liver",tabName = "liv"),
menuItem("Kidney",tabName = "kdn"),
menuItem("Poorly Perfused Tissue",tabName = "spf"),
menuItem("Richly Perfused Tissue",tabName = "rpf")
)
)
###############################Chemical Sidebar
chem_sidebar <- shinydashboard::dashboardSidebar()
###########################plots-Body
plot_body <- fluidPage(
tabItem(tabName = "plots",
fluidRow(
bsCollapse(id="plts", multiple = TRUE,
bsCollapsePanel(title = "Exposure Plots", style = "primary",
column(3,
wellPanel(
checkboxInput("ch_dose", "Instaneous Dose", value = TRUE, width = NULL),
checkboxInput("ch_totdose", "Total Dose", value = TRUE, width = NULL)
)
),
column(9,
tabBox(width=12, height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
column(4,offset = 4,
radioButtons("r_expo_type",label = "Select Exposure",inline = TRUE,
choices = c("Active"="act","All"="all"),
selected = "act"))
),
fluidRow(
plotly::plotlyOutput("exposureplt")
)
),
tabPanel("Table",
DT::DTOutput("expotble"),
downloadButton("expodwnld",label = "Get Data")))
)),
bsCollapsePanel(title = "Concentration Plots", style = "primary",
column(3,
tabsetPanel(
tabPanel("Model",value = "model",
shinyWidgets::multiInput("cplt_comp",label = tags$h4("Select Compartment"),
choices = list("Total Fat"="fat",
"Total Liver"="liv",
"Total Kidney"="kdn",
"Total Rapidly Perfused"="rpf",
"Total Slowly Perfused "="spf",
"Total Metabolite"="met"
)
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$h4("Select Datasets"),
choices = c("No Dataset"="none"),
selected = "none")
)
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_cplt_type",label = "Concentration Units",inline = TRUE,
choices = c("mg/L"="mgl","\u00B5Molar"="um"),
selected = "um")
)
),
fluidRow(
plotly::plotlyOutput("concplt")
)
),
tabPanel("Table",
DT::DTOutput("conctble"),
downloadButton("cdwnld",label ="Get Data"))
))),
bsCollapsePanel(title = "Mass Balance Plots", style = "primary",
column(8, offset = 2,
tabBox(width = 12, height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
plotOutput("balplt")
)
),
tabPanel("Table",
DT::DTOutput("baltble"),
downloadButton("cmbaldwnld",label ="Get Data"))
))
)
)
))
)
#####################compartment Body
comp_body <- dashboardBody(
tabItems(
tabItem(
tabName = "physiolocal_parameters",
fluidRow(
column(4,
selectInput("ms_org", label = "Organism",
choices = list("Trout" = "tr","Catfish"="cf"),
selected = "tr")
),
column(4,
numericInput("ms_bw","Body Weight (kg)",1,0.1,90,0.1)),
column(4,
numericInput("ms_qc","Cardiac Output (L/h)",2.06,1,50,0.1))
),
fluidRow(
column(4,
numericInput("ms_qg","Effective respiratory rate (L/h)",
min =0 , max =10, value =7.2)),
column(4,
numericInput("ms_pbldw", label = "Blood-Water Partition Coefficient",
value = 5.17, min = 0)
))),
tabItem(
tabName = "fat",
fluidRow(
column(6,
numericInput("ms_vfatc","Volume (L)",min =0, max = 1, value =0.098, step = 0.01)),
column(6,
numericInput("ms_qfatc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.085))
),
fluidRow(class="",
column(6,
numericInput("ms_pfat","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "liv",
fluidRow(
column(6,
numericInput("ms_vlivc","Volume (L)",min =0, max = 1, value =0.012, step = 0.01)),
column(6,
numericInput("ms_qlivc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1,
value =0.029))
),
fluidRow(class="",
column(6,
numericInput("ms_pliv","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "kdn",
fluidRow(
column(6,
numericInput("ms_vkdnc","Volume (L)",min =0, max = 1, value =0.009, step = 0.01)),
column(6,
numericInput("ms_qkdnc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.056))
),
fluidRow(class="",
column(6,
numericInput("ms_pkdn","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "rpf",
fluidRow(
column(6,
numericInput("ms_vrpfc","Volume (L)",min =0, max = 1, value =0.063, step = 0.01)),
column(6,
numericInput("ms_qrpfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.23))
),
fluidRow(class="",
column(6,
numericInput("ms_prpf","Partition Coefficient",1,0,2, 0.01)))
),
tabItem(
tabName = "spf",
fluidRow(
column(4,
numericInput("ms_vspfc","Volume (L)",min =0, max = 1, value =0.818, step = 0.01)),
column(4,
numericInput("ms_qspfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.6))
),
fluidRow(class="",
column(6,
numericInput("ms_pspf","Partition Coefficient",1,0,2, 0.01)))
)
)
)
####################chemical Body
chem_body <- dashboardBody(
fluidPage(id="Chemicals",
tags$h4("Chemical Parameters", class="pager-header"),
fluidRow(
column(6,
numericInput("ms_mw","Molecular Weight (g/mol)",167.8,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_vmax",paste0("Maximum Metabolism Rate (mg/h) or Intrinsic Clearance (L/h)"),0,0,250,0.01)),
column(6,
numericInput("ms_km","Michaelis-Menten Constant for Metabolism (mg/L) or -1 if Using Intrinsic Clearance",0,0,250,0.01))
),
# fluidRow(
# column(6,
# numericInput("ms_intcl", "Intrinsic Clearance (L/h)", 0,250,0.01))
# ),
# fluidRow(
# column(6,
# checkboxInput("ms_useIntcl", paste0("","Use Intrinsic Clearance",sep="\n"), value = FALSE))
# )
))
######################exposure Body
expo_body <- dashboardBody(
tabItems(
tabItem(
tabName = "ins",
fluidRow(
column(4,
numericInput("ms_cins",label="Concentration in Water (mg/L)",
value =1.062,
step= 0.01)
)
)
)
)
)
#################Shiny UI
shinyUI(fluidPage(
shinyjs::useShinyjs(),
shinyWidgets::useSweetAlert(),
theme = shinythemes::shinytheme("spacelab"),
includeCSS("www/styles.css"),
shinyjs::extendShinyjs(text = jscode, functions = c("disableTab", "enableTab")),
shinyjs::inlineCSS(css),
titlePanel(title="", windowTitle = "PLETHEM rapidPBPK"),
tags$head(
tags$meta(charset="utf-8"),
tags$meta(name="viewport", content="width=device-width, initial-scale=1"),
tags$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
#rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,
tabPanel("",value = "Home",icon =icon("home"),
includeHTML("www/home.html")),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$h4("Overwrite existing Parameter Set ?")),
column(2,
bsButton("exposave_yes","Yes",block = TRUE))
)),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 9, offset = 0,
selectizeInput("sel_expo",NULL,
choices = NULL,
options= list(placeholder = "Exposure Parameter Set",
openOnFocus = T))),
column(width = 3, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_sverest_expo","btn_saveas_expo"),
c("Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
expo_sidebar,
expo_body
)
)
)
),
tabPanel("Chemical",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 7, offset = 0,
selectizeInput("sel_chem",NULL,
choices = NULL,
options= list(placeholder = "Chemicals",
openOnFocus = T))),
column(width = 5, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_chem","btn_sverest_chem","btn_saveas_chem"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
chem_sidebar,
chem_body
)
))
),
tabPanel("Physiological",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 9, offset = 0,
selectizeInput("sel_physio",NULL,
choices = NULL,
options= list(placeholder = "Physiological Parameter Set",
openOnFocus = T))),
column(width = 3, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_physio","btn_sverest_physio","btn_saveas_physio"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
comp_sidebar,
comp_body
)
)
)
),
tabPanel("Uncertanity and Variability",
dashboardPage(
dashboardHeader(disable = T),
dashboardSidebar(
shinydashboard::sidebarMenu(
menuItem("Physiological",
tabName = "var_physio"),
menuItem("Chemical",
tabName = "var_chem"),
menuItem("Exposure",
tabName = "var_expo")
)
),
dashboardBody(tabItems(
tabItem(tabName = "var_physio",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_physio_var",NULL,
choices = NULL,
options= list(placeholder = "Population Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varphys","btn_edit_varphys","btn_import_varphys"),
c("New","Edit","Import"),
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("physio_var_tble")
)
)
),
tabItem(tabName = "var_chem",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_chem_var",NULL,
choices = NULL,
options= list(placeholder = "Chemical Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varchem","btn_edit_varchem","btn_import_varchem"),
c("New","Edit","Import"),
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("chem_var_tble"))
)
),
tabItem(tabName = "var_expo",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_expo_var",NULL,
choices = NULL,
options= list(placeholder = "Exposure Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varexpo","btn_edit_varexpo","btn_import_varexpo"),
c("New","Edit","Import"),
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("expo_var_tble"))
)
)
)
)
)
),
tabPanel("Simulations",
fluidPage(
fluidRow(tags$h4("")),
fluidRow(
column(5,
shinyWidgets::dropdownButton(
tagList(
textInput("sim_name","Name"),
textAreaInput("sim_descrp","Description",rows = 2,resize = "none"),
fluidRow(
column(6,
selectizeInput("sel_set_chem","Select Chemical",choices = NULL)
),
column(6,
selectizeInput("sel_set_chemvar","Select Variability",choices = NULL)
)
),
fluidRow(
column(6,
selectizeInput("sel_set_expo","Select Exposure",choices = NULL)
),
column(6,
selectizeInput("sel_set_expovar","Select Variability",choices = NULL)
)
),
fluidRow(
column(6,
selectizeInput("sel_set_physio","Select Compartment",choices = NULL)
),
column(6,
selectizeInput("sel_set_physiovar","Select Variability",choices = NULL)
)
),
fluidRow(
column(4,
numericInput("sim_start","Simulation Start Time (h)",0)
),
column(4,
numericInput("sim_dur","Simulation Duration (h)",0)
),
column(4,
numericInput("mc_num","Number of Monte Carlo Runs",1000)
)
),
checkboxInput("mc_mode","Run Monte Carlo Simulation",T),
shinyWidgets::actionBttn("save_sim",NULL,
icon = icon("floppy-save",lib = "glyphicon"),
style = "material-circle")
),
icon = icon("plus"),circle = F,
tooltip = F,size = "default",right = F,
width = validateCssUnit("100%"),
label = "Create new simulation",
status = "default" )),
column(3,
shinyBS::bsButton("run_sim","Run Simulation",
style = "primary",block = TRUE))
),
fluidRow(
br(),
selectizeInput("sel_sim", "Select a Simulation",
choices =NULL, width = validateCssUnit("99%"))
),
fluidRow(
wellPanel(id= "Simulationdetails1",
fluidRow(
column(8,offset =2,
tags$h4("Simulation Description"),
textOutput("sim_descrp")
)
),
fluidRow(
column(6,
tags$h4("Simulation Start (h)"),
textOutput("sim_start")
),
column(6,
tags$h4("Simulation Duration (h)"),
textOutput("sim_dur")
)
),
fluidRow(
column(6,
tags$h4("Chemical Name"),
textOutput("sim_chem")
),
column(4,
tags$h4("Exposure Name"),
textOutput("sim_expo")
)
)#,
# fluidRow(
# column(4,
# tags$h4("Age"),
# textOutput("sim_age")
# ),
# column(4,
# tags$h4("Gender"),
# textOutput("sim_gender")
# )
# ),
# fluidRow(
# column(4,
# tags$h4("Metabolism Type"),
# textOutput("sim_metab_type")
# ),
# column(4,
# tags$h4("Value"),
# textOutput("sim_metab_val")
# ),
# column(4,
# tags$h4("Units"),
# textOutput("sim_metab_units")
# )
#
# )
)
)
))
)),
tabPanel("Model Output",icon = icon("line-chart"),value = "output",
fluidRow(
column(2,
bsButton("btnAddData","Add Dataset",block = TRUE,style = "primary")
),
column(3, offset= 6,
downloadButton("downloadModel", "Download Model",class = "btn btn-primary btn-block")
),
column(1,
shinyBS::bsButton("btnOutputIntro", "Need help?",block = TRUE,style = "info"))
),
tabsetPanel(id = "Modeloutput", type = "tabs",
tabPanel("Plots",
plot_body
),
tabPanel("Parameters",
fluidPage(
fluidRow(
box(title = "Exposure Parameters",width = 4,
DT::DTOutput("expo_params_tble")),
box(title = "Chemical Specific Parameters",width = 4,
DT::DTOutput("chem_params_tble")),
box(title = "Physiological Parameters",width = 4,
DT::DTOutput("physio_params_tble"))
),
fluidRow(
downloadButton("btn_param_dwnld",
label = "Download All Paramters")
))
)
)
),
tabPanel( id = "help" , title= "help", value = "Help", icon = icon("info")),
tabPanel(title = "Quit",value = "stop",icon=icon("power-off"))
)
))
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