inst/httk_pbtk/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 = $('#'+name);
tab.unbind('click.tab');
tab.removeClass('disabled-comp');
}
"
css <- "div .disabled-comp {
color: #aaa !important;
border-color: #a00 !important;
background-color: #a00 !important;
}"
################################exposure sidebar
expo_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="ms_expo_sidebar",
tags$div(actionButton("clear_expo","Reset exposures")),
menuItem("Oral", tabName = "oral", selected = TRUE),
menuItem("Intravenous", tabName = "iv")
))
################################compartment sidebar
comp_sidebar <- shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(id="compsidebar",
menuItem(tags$h5(tags$span(style = "color:white",
"Physiological Parameters")),
tabName = "physiolocal_parameters", selected = TRUE),
menuItem("Blood",tabName="blood"),
menuItem("Gut",tabName = "gut"),
menuItem("Liver",tabName = "liver"),
menuItem("Kidney",tabName = "kidney"),
menuItem("Lungs",tabName="lung"),
menuItem("Rest of the body",tabName="rob")
)
)
###############################Chemical Sidebar
chem_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="chem_sidebar",
selectizeInput("qsarModelChem", "Select A QSAR Model",
choices = c("QSAR Model One" = 'one',
"QSAR Model Two" = 'two'),
width = "99%"),
shinyBS::bsButton("qsar4chem_props","Calculate Chemical Params",style = "primary"),
shinyBS::bsButton("btn_ivive_chem","Perform IVIVE",style = "primary")
)
#actionButton("newChem", "Modify Chemical DB"),
#selectizeInput("selectedChem", "Select a chemical", choices = getAllMainChemicals(), width = validateCssUnit("99%")),
#awesomeCheckbox("useQSar", "Use QSAR Model", value = FALSE),
)
###########################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$h4("Select Compartment"),
choices = list("Arterial Blood"="art_bld","Venous Blood"="ven_bld",
"Plasma"="to_plasma",
"Lungs"="to_lng",
"Gut"="to_gut",
"Liver"="to_liv",
"Kidney"="to_kdn",
"Rest of the Body"="to_rest"
)
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$h4("Select Datasets"),
choices = c("No Dataset"="none"),#,
selected = "none")
)
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_cplt_type",label = "Concentration Units",inline = TRUE,
choices = c("mg/L"="mgl","\u00B5Molar"="um"),
selected = "um")
)
),
fluidRow(
plotly::plotlyOutput("concplt")
)
),
tabPanel("Table",
DT::DTOutput("conctble"),
downloadButton("cdwnld",label ="Get Data"))
))
),
bsCollapsePanel(title = "Amount Plots", style = "primary",
column(3,
wellPanel(
multiInput("aplt_comp",label = tags$h4("Select Compartment"),
choices = list("Amount in Gut Lumen"="agutlumen",
"Amount Metabolized"="ametab",
"Amount in Renal Tubules"="atubules")
)
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_aplt_type",label = "Concentration Units",inline = TRUE,
choices = c("mg"="mg","\u00B5moles"="um"))
)
),
fluidRow(
plotly::plotlyOutput("amtplt")
)
),
tabPanel("Table",
DT::DTOutput("amttble"),
downloadButton("amwnld",label ="Get Data"))
))
)
# bsCollapsePanel(title = "AUC Plots", style = "primary",
# column(3,
# wellPanel(
# multiInput("aucplt_comp",label = tags$h4("Select Compartment"),
# choices = list("Blood"=c("Aretial Blood"="art_bld","Venous Blood"="ven_bld"),
# "Fat"=c("Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat"),
# "Skin"=c("Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn"),
# "Bone"=c("Bone Total"="bl_skn","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne"),
# "Muscle"=c("Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc"),
# "Brain"=c("Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn"),
# "Lungs"=c("Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng"),
# "Heart"=c("Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt"),
# "GI"=c("GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi"),
# "Liver"=c("Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv"),
# "Kidney"=c("Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn"),
# "Rapidly Perused"=c("Rapidly Perused Total"="to_rpf",
# "Rapidly Perused Tissue"="ti_rpf","Rapidly Perused Exchange"="bl_rpf"),
# "Slowly Perused"=c("Slowly Perused Total"="to_spf",
# "Slowly Perused Tissue"="ti_spf","Slowly Perused Exchange"="bl_spf")
# )
# )
# )
# ),
# column(9,
# tabBox(width = 12, height = validateCssUnit("100%"),
# tabPanel("Plot",
# fluidRow(
# plotOutput("aucplt")
# )
# ),
# tabPanel("Table",
# dataTableOutput("auctble"),
# downloadButton("aucdwnld",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(
# dropdown(
# pickerInput("comp_sel","Select Organism",inline = TRUE,choices = NULL,options= list(title = "Add Compartment")),
# actionBttn("add_comp",NULL,style = "material-circle",color = "primary", icon = icon("plus"))
#
# ),
tabItems(
tabItem(
tabName = "physiolocal_parameters",
fluidRow(
# column(4,
# selectInput("ms_Org", label = "Organism",
# choices = list("Human" = "Human","Rat"= "Rat"),
# selected = "Human")
# ),
column(6,
selectInput("ms_Gender", label = "Gender",
choices = list("Male" = "M", "Female" = "F"),
selected = "M")
),
column(6,
numericInput("ms_Age","Age",25,0.5,80,1)
)
),
fluidRow(
column(4,
numericInput("ms_BW","Body Weight (kg)",70,0.1,90,0.1)),
column(4,
numericInput("ms_Qcardiacc","Cardiac Output (L/h)",420,1,50,0.1)),
column(4,
numericInput("ms_hematocrit","Hematocrit Factor",0.441,0,1,0.001))
),
fluidRow(
column(4,
numericInput("ms_Qgfrc","Glomerular Filteration (L/h/kg BW)",min =0 , max =1, value =0.08)
),
column(4,
numericInput("ms_Fgutabs","Fraction of the Oral Dose Absorbed",1)
),
column(4,
numericInput("ms_kgutabs","Rate of Absorption into Gut (1/h)",1)
)
)
),
tabItem(
tabName = "gut",
fluidRow(
column(6,
numericInput("ms_Vgutc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qgutf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Kgut2pu","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "liver",
fluidRow(
column(6,
numericInput("ms_Vliverc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qliverf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Kliver2pu","Partition Coefficient",0.5,0,2, 0.01)
),
column(6,
numericInput("ms_million.cells.per.gliver","Hepatocellularity",110)
)
),
fluidRow(
column(6,
numericInput("ms_Fhep.assay.correction","Hepatocyte Assay Correction",1)
)
)
),
tabItem(
tabName = "blood",
fluidRow(
column(6,
numericInput("ms_Vartc","Arterial Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)
),
column(6,
numericInput("ms_Vvenc","Venous Volume Ratio",min =0 , max =1, value =0.1139)
)
),
fluidRow(class="",
column(6,
numericInput("ms_Krbc2pu","RBC to Plasma Partition Coefficient",0.5,0,2, 0.01)
)
)
),
tabItem(
tabName = "kidney",
fluidRow(
column(6,
numericInput("ms_Vkidneyc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qkidneyf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Kkidney2pu","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "lung",
fluidRow(
column(6,
numericInput("ms_Vlungc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qlungf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Klung2pu","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "rob",
fluidRow(
column(6,
numericInput("ms_Vrestc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qrestf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Krest2pu","Partition Coefficient",0.5,0,2, 0.01)))
)
)
)
####################chemical Body
chem_body <- dashboardBody(
fluidPage(id="Chemicals",
tags$h4("Chemical Parameters", class="pager-header"),
fluidRow(
column(6,
selectInput("ms_Corg","Organism",choices = list("Human"="Human","Rat"="Rat"))
),
column(6,
numericInput("ms_Clint","Instrinsic Clearance",1))
),
fluidRow(
column(6,
numericInput("ms_LogMA","Membrane Affinity",1)),
column(6,
numericInput("ms_MW","Molecular Weight (g/mol)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_LogP","Octanol-water partition Coefficient",1,0,250,0.01)),
column(6,
numericInput("ms_LogPwa","Water-air Partition Coefficient",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_pKa_Accept","Accept Pka",1,0,250,0.01)),
column(6,
numericInput("ms_pKa_Donor","Donor Pka",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_Clmetabolismc","First Order metabolism in Liver (L/h/kg BW)",1)
),
column(6,
numericInput("ms_Funbound.plasma", label = "Fraction Unbound in Palsma", value = 1, 0, 1, 0.001))
),
fluidRow(
column(6,
numericInput("ms_Rblood2plasma","Ratio of Chemical in Blood to Plasma",1)
)
)
)
)
######################exposure Body
expo_body <- dashboardBody(
tabItems(
tabItem(
tabName = "oral",
fluidRow(
column(6,
numericInput("ms_bdose",label="Daily Oral Dose (mg/kg BW)", value =0, step= 0.01)),
column(6,
numericInput("ms_blen",label = "Total length of dosing (h/day)", value = 1, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_breps","Number of Bolus Doses",0,0,100, 1)),
column(6,
awesomeCheckbox("ms_brep_flag","Repeat Dose Daily?",value = F))
)
),
tabItem(tabName ="dw",
fluidRow(
column(6,
numericInput("ms_drdose",label = "Chemical Concentration (mg/L)", value = 0, step = 0.1)),
column(6,
numericInput("ms_vdw", "Volume of Drinking Water per Bolus (L)", value = 0, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_dreps", "Number of drinking water doses per day", value = 1, step = 0.1 )
)
)
),
tabItem(
tabName = "inh",
fluidRow(
column(4,
numericInput("ms_inhdose",label="Inhalation Dose (ppm)", value =0, step= 0.01)),
column(4,
numericInput("ms_inhtlen",label = "Length of Inhalation Dose (h)",0)),
column(4,
numericInput("ms_inhdays",label = "Days of dosing in a week",7))
)
),
tabItem(
tabName = "iv",
fluidRow(
column(6,
numericInput("ms_ivdose",label = "IV Dose (mg/h)",value = 0,step = 0.01)
),
column(6,
numericInput("ms_ivlen",label="Length of IV Dose (h)",0))
),
fluidRow(
column(6,
awesomeCheckbox("ms_ivrep_flag","Repeat Dose Daily?",value = F))
)
)
)
)
#################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$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,
tabPanel("",value = "Home",icon =icon("home"),
includeHTML("www/home.html")),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
# fluidRow(
# column(4,
# bsButton("run","Run Simulation", style = "primary", block = TRUE)
# ),
# column(2,
# bsButton("btnSetupIntro", "Need help?", style = "default", size = "medium", block = TRUE)
# )
# ),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$h4("Overwrite existing Parameter Set ?")),
column(2,
bsButton("exposave_yes","Yes",block = TRUE))
)),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(2,
shinyBS::bsButton("btn_seem_upload",
"Import From SEEM Data",
block = T))
),
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"),
c("Import"),
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(
# column(2,
# shinyBS::tipify(shinyBS::bsButton("btn_use_lifecourse",
# "Calculate Parameters",
# style = "primary",block = TRUE),
# "Use Lifecourse Equation to calcualte parameters")
# ),
column(4,
selectInput("ms_Org", NULL,
#label = "Organism",
choices = list("Human" = "Human","Rat"= "Rat"),
selected = "Human")
# shinyBS::tipify(selectizeInput("sel_qsar4Partition", NULL,
# choices = c("QSAR Model One" = 'one',
# "QSAR Model Two" = 'two')
# ),
# "Select QSAR model for partition coefficients")
),
column(6,
shinyBS::tipify(selectizeInput("sel_chem4Partition",NULL,
choices ="No Chemical Added"
),
"Select Chemical for qsar model")
),
column(2,
shinyBS::bsButton("btn_useQSAR4Partition",
"Parameterize Model",
#"Calculate Partition",
style = "primary",
block = TRUE)
)
),
fluidRow(
column(12,
div(style = "height:5px")
)
),
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 = "Metabolism 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,
tableOutput("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,
tableOutput("expo_var_tble"))
)
)
)
)
)
),
# tabPanel("Metabolism",
#
# fluidPage(
# fluidRow(
# column(12,
# div(style = "height:10px")
# )
# ),
# fluidRow(
#
# column(2,
# bsButton("btn_metab_upload",
# "Upload Metabolism Files",
#
# block = T)
# )
# ),
# fluidRow(
# column(12,
# div(style = "height:10px")
# )
# ),
# fluidRow(
# column(width = 7, offset = 0,
# selectizeInput("sel_metab",NULL,
# choices = NULL,
# options= list(placeholder = "Metabolism Parameter Set",
# openOnFocus = T))),
# column(width = 5, offset = 0,
# shinyWidgets::actionGroupButtons(
# c("btn_sve_metab","btn_saveas_metab"),
# c("Save","Save As"),
# direction = "horizontal",
# status = "info",
# fullwidth = T
#
# ))
# ),
# fluidRow(
# column(12,
# div(style = "height:10px")
# )
# ),
# # fluidRow(
# # column(width = 3,
# # fileInput("metab_csv","Upload Metabolism Data")),
# # column(width = 3,
# # downloadLink("metab_template","Template for metabolism file"))
# # ),
# # fluidRow(
# # column(width = 4,
# # textInput("metab_set_name","Name",
# # placeholder = "Enter the name for this metabolism set")),
# # column(width = 8,
# # textAreaInput("metab_set_descrp","Description",
# # resize = "none" ,row = 1))
# #
# # ),
# # fluidRow(column(width = 6,
# # shinyWidgets::radioGroupButtons("metab_type",justified = T,
# # "Select Meatbolism Type",
# # choices = c("VmaxC"="m1","VlivC"="m2"))
# # )
# #
# #
# #
# # ),
# # fluidRow(column(width = 4,
# # shinyWidgets::awesomeCheckbox("use_ref",
# # "Use clearance at reference age for ages not in the metabolism table",
# # value = T)
# # ),
# # column(width = 4,
# # numericInput("metab_ref_age","Referance age in Years",value = 25, min = 0))
# # ),
# fluidRow(column(width = 6, offset = 3,
# DT::DTOutput("metab_tble")))
#
#
# )
#
# ),
tabPanel("Simulations",
fluidPage(
# fluidRow(tags$h4("")),
# fluidRow(
#
# column(1,
# shinyWidgets::actionBttn("add_row",NULL,
# icon = icon("plus"),style = "material-circle",
# block = TRUE)
# ),
# column(1,
# shinyWidgets::actionBttn("rem_row",NULL,
# icon = icon("remove"),style = "material-circle",
# block = TRUE)
# ),
# column(10,
# actionButton("run_row","Run Selected Row",width = validateCssUnit("100%")))
# ),
fluidRow(tags$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)
)
),
selectizeInput("sel_set_metab","Select Metabolism",choice = NULL),
fluidRow(
column(6,
numericInput("sim_dur","Simulation Duration (days)",0)
),
column(6,
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%"))
# bsCollapse(id = "sim_selector",multiple = TRUE, open ="Simulations",
# # bsCollapsePanel("Chemicals",style = "primary",
# # selectizeInput("sim_chem_filter", "Select a chemical",
# # choices = NULL,
# # width = validateCssUnit("99%"))
# # ),
# # bsCollapsePanel("Exposure",style = "primary",
# # radioButtons("sim_expo_type",label = NULL,
# # choices = c("Oral"="oral",
# # "Drinking Water"="dw",
# # "Inhalation"="inh",
# # "Intravenous"="derm"),
# # selected = 'oral',
# # inline = FALSE,
# # width = validateCssUnit("100%"))
# # ),
# bsCollapsePanel("Simulations",style = "primary",
# selectizeInput("sel_sim", "Select a Simulation",
# choices =NULL, width = validateCssUnit("99%"))
# )
# )
),
fluidRow(
wellPanel(id= "Simulationdetails",
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$h4("Simulation Duration (days)"),
textOutput("sim_dur")
)
),
fluidRow(
column(6,
tags$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 Parameters",width = 4,
DT::DTOutput("pamamstbl")),
box(title = "Physiological Parameters",width = 4,
DT::DTOutput("physio_params_tble"))
# tags$h3("CURRENT PARAMETERS", class="text-center page-header"),
# column(10, offset = 1, id="paramsCurrentValues",
# dataTableOutput("pamamstbl")
# )
),
fluidRow(
downloadButton("btn_param_dwnld",
label = "Download All Paramters")
))
)
)
),
tabPanel( id = "help" , title= "help", value = "Help", icon = icon("info")),
tabPanel(title = "",value = "Stop",icon=icon("power-off"))
)
))
ScitoVation/plethem documentation built on Oct. 1, 2020, 3:37 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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 = $('#'+name);
tab.unbind('click.tab');
tab.removeClass('disabled-comp');
}
"
css <- "div .disabled-comp {
color: #aaa !important;
border-color: #a00 !important;
background-color: #a00 !important;
}"
################################exposure sidebar
expo_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="ms_expo_sidebar",
tags$div(actionButton("clear_expo","Reset exposures")),
menuItem("Oral", tabName = "oral", selected = TRUE),
menuItem("Intravenous", tabName = "iv")
))
################################compartment sidebar
comp_sidebar <- shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(id="compsidebar",
menuItem(tags$h5(tags$span(style = "color:white",
"Physiological Parameters")),
tabName = "physiolocal_parameters", selected = TRUE),
menuItem("Blood",tabName="blood"),
menuItem("Gut",tabName = "gut"),
menuItem("Liver",tabName = "liver"),
menuItem("Kidney",tabName = "kidney"),
menuItem("Lungs",tabName="lung"),
menuItem("Rest of the body",tabName="rob")
)
)
###############################Chemical Sidebar
chem_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="chem_sidebar",
selectizeInput("qsarModelChem", "Select A QSAR Model",
choices = c("QSAR Model One" = 'one',
"QSAR Model Two" = 'two'),
width = "99%"),
shinyBS::bsButton("qsar4chem_props","Calculate Chemical Params",style = "primary"),
shinyBS::bsButton("btn_ivive_chem","Perform IVIVE",style = "primary")
)
#actionButton("newChem", "Modify Chemical DB"),
#selectizeInput("selectedChem", "Select a chemical", choices = getAllMainChemicals(), width = validateCssUnit("99%")),
#awesomeCheckbox("useQSar", "Use QSAR Model", value = FALSE),
)
###########################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$h4("Select Compartment"),
choices = list("Arterial Blood"="art_bld","Venous Blood"="ven_bld",
"Plasma"="to_plasma",
"Lungs"="to_lng",
"Gut"="to_gut",
"Liver"="to_liv",
"Kidney"="to_kdn",
"Rest of the Body"="to_rest"
)
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$h4("Select Datasets"),
choices = c("No Dataset"="none"),#,
selected = "none")
)
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_cplt_type",label = "Concentration Units",inline = TRUE,
choices = c("mg/L"="mgl","\u00B5Molar"="um"),
selected = "um")
)
),
fluidRow(
plotly::plotlyOutput("concplt")
)
),
tabPanel("Table",
DT::DTOutput("conctble"),
downloadButton("cdwnld",label ="Get Data"))
))
),
bsCollapsePanel(title = "Amount Plots", style = "primary",
column(3,
wellPanel(
multiInput("aplt_comp",label = tags$h4("Select Compartment"),
choices = list("Amount in Gut Lumen"="agutlumen",
"Amount Metabolized"="ametab",
"Amount in Renal Tubules"="atubules")
)
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_aplt_type",label = "Concentration Units",inline = TRUE,
choices = c("mg"="mg","\u00B5moles"="um"))
)
),
fluidRow(
plotly::plotlyOutput("amtplt")
)
),
tabPanel("Table",
DT::DTOutput("amttble"),
downloadButton("amwnld",label ="Get Data"))
))
)
# bsCollapsePanel(title = "AUC Plots", style = "primary",
# column(3,
# wellPanel(
# multiInput("aucplt_comp",label = tags$h4("Select Compartment"),
# choices = list("Blood"=c("Aretial Blood"="art_bld","Venous Blood"="ven_bld"),
# "Fat"=c("Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat"),
# "Skin"=c("Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn"),
# "Bone"=c("Bone Total"="bl_skn","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne"),
# "Muscle"=c("Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc"),
# "Brain"=c("Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn"),
# "Lungs"=c("Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng"),
# "Heart"=c("Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt"),
# "GI"=c("GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi"),
# "Liver"=c("Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv"),
# "Kidney"=c("Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn"),
# "Rapidly Perused"=c("Rapidly Perused Total"="to_rpf",
# "Rapidly Perused Tissue"="ti_rpf","Rapidly Perused Exchange"="bl_rpf"),
# "Slowly Perused"=c("Slowly Perused Total"="to_spf",
# "Slowly Perused Tissue"="ti_spf","Slowly Perused Exchange"="bl_spf")
# )
# )
# )
# ),
# column(9,
# tabBox(width = 12, height = validateCssUnit("100%"),
# tabPanel("Plot",
# fluidRow(
# plotOutput("aucplt")
# )
# ),
# tabPanel("Table",
# dataTableOutput("auctble"),
# downloadButton("aucdwnld",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(
# dropdown(
# pickerInput("comp_sel","Select Organism",inline = TRUE,choices = NULL,options= list(title = "Add Compartment")),
# actionBttn("add_comp",NULL,style = "material-circle",color = "primary", icon = icon("plus"))
#
# ),
tabItems(
tabItem(
tabName = "physiolocal_parameters",
fluidRow(
# column(4,
# selectInput("ms_Org", label = "Organism",
# choices = list("Human" = "Human","Rat"= "Rat"),
# selected = "Human")
# ),
column(6,
selectInput("ms_Gender", label = "Gender",
choices = list("Male" = "M", "Female" = "F"),
selected = "M")
),
column(6,
numericInput("ms_Age","Age",25,0.5,80,1)
)
),
fluidRow(
column(4,
numericInput("ms_BW","Body Weight (kg)",70,0.1,90,0.1)),
column(4,
numericInput("ms_Qcardiacc","Cardiac Output (L/h)",420,1,50,0.1)),
column(4,
numericInput("ms_hematocrit","Hematocrit Factor",0.441,0,1,0.001))
),
fluidRow(
column(4,
numericInput("ms_Qgfrc","Glomerular Filteration (L/h/kg BW)",min =0 , max =1, value =0.08)
),
column(4,
numericInput("ms_Fgutabs","Fraction of the Oral Dose Absorbed",1)
),
column(4,
numericInput("ms_kgutabs","Rate of Absorption into Gut (1/h)",1)
)
)
),
tabItem(
tabName = "gut",
fluidRow(
column(6,
numericInput("ms_Vgutc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qgutf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Kgut2pu","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "liver",
fluidRow(
column(6,
numericInput("ms_Vliverc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qliverf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Kliver2pu","Partition Coefficient",0.5,0,2, 0.01)
),
column(6,
numericInput("ms_million.cells.per.gliver","Hepatocellularity",110)
)
),
fluidRow(
column(6,
numericInput("ms_Fhep.assay.correction","Hepatocyte Assay Correction",1)
)
)
),
tabItem(
tabName = "blood",
fluidRow(
column(6,
numericInput("ms_Vartc","Arterial Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)
),
column(6,
numericInput("ms_Vvenc","Venous Volume Ratio",min =0 , max =1, value =0.1139)
)
),
fluidRow(class="",
column(6,
numericInput("ms_Krbc2pu","RBC to Plasma Partition Coefficient",0.5,0,2, 0.01)
)
)
),
tabItem(
tabName = "kidney",
fluidRow(
column(6,
numericInput("ms_Vkidneyc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qkidneyf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Kkidney2pu","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "lung",
fluidRow(
column(6,
numericInput("ms_Vlungc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qlungf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Klung2pu","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "rob",
fluidRow(
column(6,
numericInput("ms_Vrestc","Volume Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_Qrestf","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_Krest2pu","Partition Coefficient",0.5,0,2, 0.01)))
)
)
)
####################chemical Body
chem_body <- dashboardBody(
fluidPage(id="Chemicals",
tags$h4("Chemical Parameters", class="pager-header"),
fluidRow(
column(6,
selectInput("ms_Corg","Organism",choices = list("Human"="Human","Rat"="Rat"))
),
column(6,
numericInput("ms_Clint","Instrinsic Clearance",1))
),
fluidRow(
column(6,
numericInput("ms_LogMA","Membrane Affinity",1)),
column(6,
numericInput("ms_MW","Molecular Weight (g/mol)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_LogP","Octanol-water partition Coefficient",1,0,250,0.01)),
column(6,
numericInput("ms_LogPwa","Water-air Partition Coefficient",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_pKa_Accept","Accept Pka",1,0,250,0.01)),
column(6,
numericInput("ms_pKa_Donor","Donor Pka",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_Clmetabolismc","First Order metabolism in Liver (L/h/kg BW)",1)
),
column(6,
numericInput("ms_Funbound.plasma", label = "Fraction Unbound in Palsma", value = 1, 0, 1, 0.001))
),
fluidRow(
column(6,
numericInput("ms_Rblood2plasma","Ratio of Chemical in Blood to Plasma",1)
)
)
)
)
######################exposure Body
expo_body <- dashboardBody(
tabItems(
tabItem(
tabName = "oral",
fluidRow(
column(6,
numericInput("ms_bdose",label="Daily Oral Dose (mg/kg BW)", value =0, step= 0.01)),
column(6,
numericInput("ms_blen",label = "Total length of dosing (h/day)", value = 1, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_breps","Number of Bolus Doses",0,0,100, 1)),
column(6,
awesomeCheckbox("ms_brep_flag","Repeat Dose Daily?",value = F))
)
),
tabItem(tabName ="dw",
fluidRow(
column(6,
numericInput("ms_drdose",label = "Chemical Concentration (mg/L)", value = 0, step = 0.1)),
column(6,
numericInput("ms_vdw", "Volume of Drinking Water per Bolus (L)", value = 0, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_dreps", "Number of drinking water doses per day", value = 1, step = 0.1 )
)
)
),
tabItem(
tabName = "inh",
fluidRow(
column(4,
numericInput("ms_inhdose",label="Inhalation Dose (ppm)", value =0, step= 0.01)),
column(4,
numericInput("ms_inhtlen",label = "Length of Inhalation Dose (h)",0)),
column(4,
numericInput("ms_inhdays",label = "Days of dosing in a week",7))
)
),
tabItem(
tabName = "iv",
fluidRow(
column(6,
numericInput("ms_ivdose",label = "IV Dose (mg/h)",value = 0,step = 0.01)
),
column(6,
numericInput("ms_ivlen",label="Length of IV Dose (h)",0))
),
fluidRow(
column(6,
awesomeCheckbox("ms_ivrep_flag","Repeat Dose Daily?",value = F))
)
)
)
)
#################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$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,
tabPanel("",value = "Home",icon =icon("home"),
includeHTML("www/home.html")),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
# fluidRow(
# column(4,
# bsButton("run","Run Simulation", style = "primary", block = TRUE)
# ),
# column(2,
# bsButton("btnSetupIntro", "Need help?", style = "default", size = "medium", block = TRUE)
# )
# ),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$h4("Overwrite existing Parameter Set ?")),
column(2,
bsButton("exposave_yes","Yes",block = TRUE))
)),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(2,
shinyBS::bsButton("btn_seem_upload",
"Import From SEEM Data",
block = T))
),
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"),
c("Import"),
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(
# column(2,
# shinyBS::tipify(shinyBS::bsButton("btn_use_lifecourse",
# "Calculate Parameters",
# style = "primary",block = TRUE),
# "Use Lifecourse Equation to calcualte parameters")
# ),
column(4,
selectInput("ms_Org", NULL,
#label = "Organism",
choices = list("Human" = "Human","Rat"= "Rat"),
selected = "Human")
# shinyBS::tipify(selectizeInput("sel_qsar4Partition", NULL,
# choices = c("QSAR Model One" = 'one',
# "QSAR Model Two" = 'two')
# ),
# "Select QSAR model for partition coefficients")
),
column(6,
shinyBS::tipify(selectizeInput("sel_chem4Partition",NULL,
choices ="No Chemical Added"
),
"Select Chemical for qsar model")
),
column(2,
shinyBS::bsButton("btn_useQSAR4Partition",
"Parameterize Model",
#"Calculate Partition",
style = "primary",
block = TRUE)
)
),
fluidRow(
column(12,
div(style = "height:5px")
)
),
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 = "Metabolism 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,
tableOutput("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,
tableOutput("expo_var_tble"))
)
)
)
)
)
),
# tabPanel("Metabolism",
#
# fluidPage(
# fluidRow(
# column(12,
# div(style = "height:10px")
# )
# ),
# fluidRow(
#
# column(2,
# bsButton("btn_metab_upload",
# "Upload Metabolism Files",
#
# block = T)
# )
# ),
# fluidRow(
# column(12,
# div(style = "height:10px")
# )
# ),
# fluidRow(
# column(width = 7, offset = 0,
# selectizeInput("sel_metab",NULL,
# choices = NULL,
# options= list(placeholder = "Metabolism Parameter Set",
# openOnFocus = T))),
# column(width = 5, offset = 0,
# shinyWidgets::actionGroupButtons(
# c("btn_sve_metab","btn_saveas_metab"),
# c("Save","Save As"),
# direction = "horizontal",
# status = "info",
# fullwidth = T
#
# ))
# ),
# fluidRow(
# column(12,
# div(style = "height:10px")
# )
# ),
# # fluidRow(
# # column(width = 3,
# # fileInput("metab_csv","Upload Metabolism Data")),
# # column(width = 3,
# # downloadLink("metab_template","Template for metabolism file"))
# # ),
# # fluidRow(
# # column(width = 4,
# # textInput("metab_set_name","Name",
# # placeholder = "Enter the name for this metabolism set")),
# # column(width = 8,
# # textAreaInput("metab_set_descrp","Description",
# # resize = "none" ,row = 1))
# #
# # ),
# # fluidRow(column(width = 6,
# # shinyWidgets::radioGroupButtons("metab_type",justified = T,
# # "Select Meatbolism Type",
# # choices = c("VmaxC"="m1","VlivC"="m2"))
# # )
# #
# #
# #
# # ),
# # fluidRow(column(width = 4,
# # shinyWidgets::awesomeCheckbox("use_ref",
# # "Use clearance at reference age for ages not in the metabolism table",
# # value = T)
# # ),
# # column(width = 4,
# # numericInput("metab_ref_age","Referance age in Years",value = 25, min = 0))
# # ),
# fluidRow(column(width = 6, offset = 3,
# DT::DTOutput("metab_tble")))
#
#
# )
#
# ),
tabPanel("Simulations",
fluidPage(
# fluidRow(tags$h4("")),
# fluidRow(
#
# column(1,
# shinyWidgets::actionBttn("add_row",NULL,
# icon = icon("plus"),style = "material-circle",
# block = TRUE)
# ),
# column(1,
# shinyWidgets::actionBttn("rem_row",NULL,
# icon = icon("remove"),style = "material-circle",
# block = TRUE)
# ),
# column(10,
# actionButton("run_row","Run Selected Row",width = validateCssUnit("100%")))
# ),
fluidRow(tags$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)
)
),
selectizeInput("sel_set_metab","Select Metabolism",choice = NULL),
fluidRow(
column(6,
numericInput("sim_dur","Simulation Duration (days)",0)
),
column(6,
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%"))
# bsCollapse(id = "sim_selector",multiple = TRUE, open ="Simulations",
# # bsCollapsePanel("Chemicals",style = "primary",
# # selectizeInput("sim_chem_filter", "Select a chemical",
# # choices = NULL,
# # width = validateCssUnit("99%"))
# # ),
# # bsCollapsePanel("Exposure",style = "primary",
# # radioButtons("sim_expo_type",label = NULL,
# # choices = c("Oral"="oral",
# # "Drinking Water"="dw",
# # "Inhalation"="inh",
# # "Intravenous"="derm"),
# # selected = 'oral',
# # inline = FALSE,
# # width = validateCssUnit("100%"))
# # ),
# bsCollapsePanel("Simulations",style = "primary",
# selectizeInput("sel_sim", "Select a Simulation",
# choices =NULL, width = validateCssUnit("99%"))
# )
# )
),
fluidRow(
wellPanel(id= "Simulationdetails",
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$h4("Simulation Duration (days)"),
textOutput("sim_dur")
)
),
fluidRow(
column(6,
tags$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 Parameters",width = 4,
DT::DTOutput("pamamstbl")),
box(title = "Physiological Parameters",width = 4,
DT::DTOutput("physio_params_tble"))
# tags$h3("CURRENT PARAMETERS", class="text-center page-header"),
# column(10, offset = 1, id="paramsCurrentValues",
# dataTableOutput("pamamstbl")
# )
),
fluidRow(
downloadButton("btn_param_dwnld",
label = "Download All Paramters")
))
)
)
),
tabPanel( id = "help" , title= "help", value = "Help", icon = icon("info")),
tabPanel(title = "",value = "Stop",icon=icon("power-off"))
)
))
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