inst/rapidPBPK_pop/ui.R
In ScitoVation/plethem: Population Life Course Exposure to Health Effects Modeling
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 = $('#'+name);
tab.unbind('click.tab');
tab.removeClass('disabled-comp');
}
shinyjs.reset = function(){history.go(0)}
"
css <- "div .disabled-comp {
color: #aaa !important;
border-color: #a00 !important;
background-color: #a00 !important;
}"
################################exposure sidebar
expo_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="ms_expo_sidebar",
tags$div(
tipify(
actionButton("clear_expo","Reset Exposures"),
"Reset all exposure values to zero. This is needed before a new set can be created",
placement = "right")
),
menuItem("Oral", tabName = "oral", selected = TRUE),
menuItem("Drinking Water", tabName = "dw"),
menuItem("Oral Exposure with Vehicle",tabName = "oralv"),
menuItem("Inhalation", tabName = "inh"),
menuItem("Intravenous", tabName = "iv"),
menuItem("Dermal",tabName = "dermal")
))
################################compartment sidebar
comp_sidebar <- shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(id="compsidebar",
# tags$div(shinyWidgets::radioGroupButtons("ms_org",
# label = "Select Organism",
# choices = c("Human" = "ha","Rat"="ra"),
# selected = "ha",size = "normal",
# checkIcon = list(yes = icon('ok',lib ="glyphicon")))),
menuItem(tags$h5(tags$span(style = "color:white",
"Physiological Parameters")),
tabName = "physiolocal_parameters", selected = TRUE),
tags$div(class = "comp_checkboxes",
tags$h4(tags$span(style = "color:white","Model Compartments")),
checkboxGroupInput("ms_cmplist",NULL,
selected = c("fat","skin","muscle",
"bone","brain",
"lung","heart","gi",
"liver","kidney","rpf","spf"),
choiceNames = list(tags$div(id = "fat",class = "comp_tabs",
menuItem("Fat",tabName = "fat",
icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "fat_tissue"),
menuSubItem("Compartment",
tabName = "fat_blood")
)
),
tags$div(id = "skin",class = "comp_tabs",
menuItem("Skin",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "skin_tissue"),
menuSubItem("Compartment",
tabName = "skin_blood")
)
),
tags$div(id = "muscle",class = "comp_tabs",
menuItem("Muscle",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "muscle_tissue"),
menuSubItem("Compartment",
tabName = "muscle_blood")
)
),
tags$div(id = "bone",class = "comp_tabs",
menuItem("Bone",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "bone_tissue"),
menuSubItem("Compartment",
tabName = "bone_blood")
)
),
tags$div(id = "brain",class = "comp_tabs",
menuItem("Brain",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "brain_tissue"),
menuSubItem("Compartment",
tabName = "brain_blood")
)
),
tags$div(id = "lung",class = "comp_tabs",
menuItem("Lungs",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "lung_tissue"),
menuSubItem("Compartment",
tabName = "lung_blood")
)
),
tags$div(id = "heart",class = "comp_tabs",
menuItem("Heart",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "heart_tissue"),
menuSubItem("Compartment",
tabName = "heart_blood")
)
),
tags$div(id = "gi",class = "comp_tabs",
menuItem("GI",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "gi_tissue"),
menuSubItem("Compartment",
tabName = "gi_blood")
)
),
tags$div(id = "liver",class = "comp_tabs",
menuItem("Liver",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "liver_tissue"),
menuSubItem("Compartment",
tabName = "liver_blood")
)
),
tags$div(id = "kidney",class = "comp_tabs",
menuItem("Kidney",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "kidney_tissue"),
menuSubItem("Compartment",
tabName = "kidney_blood")
)
),
tags$div(id = "rpf",class = "comp_tabs",
menuItem("Rapidly Perfused",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "rpf_tissue"),
menuSubItem("Compartment",
tabName = "rpf_blood")
)
),
tags$div(id = "spf",class = "comp_tabs",
menuItem("Slowly Perfused",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "spf_tissue"),
menuSubItem("Compartment",
tabName = "spf_blood")
)
)
),
choiceValues = list("fat","skin","muscle",
"bone","brain",
"lung","heart","gi",
"liver","kidney","rpf","spf")
)
)
)
)
###############################Chemical Sidebar
chem_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="chem_sidebar",
pickerInput("qsarModelChem", "Select A QSAR Model",
choices = c("QSAR Model One" = 'one'),
#"Unified QSAR model" = 'two'),
width = "99%"),
tipify(shinyBS::bsButton("qsar4chem_props",
"Estimate Fraction Dissolved",
style = "primary"),
"Estimate fraction dissoved in liquid phase of plasma using QSAR Models."
)
)
)
###########################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",
fluidRow(
column(2,
bsButton("btnAddData","Add Dataset",block = TRUE,style = "primary")
)
),
fluidRow(
column(3,
tabsetPanel(
tabPanel("Model",value = "model",
shinyWidgets::multiInput("cplt_comp",label = tags$h4("Select Compartment"),
choices = list("Arterial Plasma"="art_bld","Venous Plasma"="ven_bld",
"Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat",
"Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn",
"Bone Total"="to_bne","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne",
"Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc",
"Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn",
"Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng",
"Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt",
"GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi",
"Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv",
"Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn",
"Rapidly Perfused Total"="to_rpf",
"Rapidly Perfused Tissue"="ti_rpf","Rapidly Perfused Exchange"="bl_rpf",
"Slowly Perfused Total"="to_spf",
"Slowly Perfused Tissue"="ti_spf","Slowly Perfused Exchange"="bl_spf",
"Parent Urinary Concentration"="urine","Metabolite Urinary Concentration"="meturine"
),
selected="art_bld"
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$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("Arterial Plasma"="art_bld",
"Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat",
"Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn",
"Bone Total"="to_bne","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne",
"Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc",
"Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn",
"Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng",
"Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt",
"GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi",
"Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv",
"Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn",
"Rapidly Perused Total"="to_rpf",
"Rapidly Perused Tissue"="ti_rpf","Rapidly Perused Exchange"="bl_rpf",
"Slowly Perused Total"="to_spf",
"Slowly Perused Tissue"="ti_spf","Slowly Perused Exchange"="bl_spf"
),
selected="art_bld"
)
#selectizeInput("aplt_data",tags$h4("Select Data Sets"),choices = c("a","b","c"))
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_aplt_type",label = "Amount 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 = "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("Human" = "ha","Rat"= "ra"),
selected = "ha")
),
column(4,
selectInput("ms_gender", label = "Gender",
choices = list("Male" = "M", "Female" = "F"),
selected = "M")
),
column(4,
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_qcc","Cardiac Output (L/h)",420,1,50,0.1)),
column(4,
numericInput("ms_hct","Hematocrit Factor",0.441,0,1,0.001))
),
fluidRow(
column(6,
numericInput("ms_vbldc","Fractional Blood Compartment Volume",0.0832,0.01,1,0.01)),
column(6,
numericInput("ms_perfc","Total Fractional Perfused Tissue",1,0.75,0.95,0.01)
)
),
fluidRow(
column(4,
numericInput("ms_respr","Respiration Rate (L/h)",min =0 , max =10, value =490)),
column(4,
numericInput("ms_tv","Tidal Volume (L)",min =0 , max =10, value =0.623)),
column(4,
numericInput("ms_ds","Dead Space (L)",min =0 , max =10, value =0.154))
),
fluidRow(
column(6,
numericInput("ms_uflwc","Urinary Flow Rate (L/kg/day)",min =0 , max =1, value =0.0214)),
column(6,
numericInput("ms_gfr","Glomerular Filtration (L/h)",min =0 , max =1, value =0.08)
)
)
),
tabItem(
tabName = "fat_tissue",
fluidRow(
column(6,
numericInput("ms_fatvtbc","Fat Tissue to Total Fat Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "fat_blood",
fluidRow(
column(6,
numericInput("ms_vfatc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.1841, step = 0.01)),
column(6,
numericInput("ms_qfatc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.08226))
)
),
tabItem(
tabName = "skin_tissue",
fluidRow(
column(6,
numericInput("ms_skinvtbc","Skin Tissue to Total Skin Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "skin_blood",
fluidRow(
column(6,
numericInput("ms_vskinc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0553, step = 0.01)),
column(6,
numericInput("ms_qskinc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.06783))
)
),
tabItem(
tabName = "muscle_tissue",
fluidRow(
column(6,
numericInput("ms_muscvtbc","Muscle Tissue to Total Muscle Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "muscle_blood",
fluidRow(
column(6,
numericInput("ms_vmuscc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.4576, step = 0.01)),
column(6,
numericInput("ms_qmuscc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.13711))
)
),
tabItem(
tabName = "bone_tissue",
fluidRow(
column(6,
numericInput("ms_bonevtbc","Bone Tissue to Total Bone Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "bone_blood",
fluidRow(
column(6,
numericInput("ms_vbonec","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.1318, step = 0.01)),
column(6,
numericInput("ms_qbonec","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.1266))
)
),
tabItem(
tabName = "brain_tissue",
fluidRow(
column(6,
numericInput("ms_brnvtbc","Brain Tissue to Total Brain Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "brain_blood",
fluidRow(
column(6,
numericInput("ms_vbrnc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0192, step = 0.01)),
column(6,
numericInput("ms_qbrnc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.098))
)
),
tabItem(
tabName = "lung_tissue",
fluidRow(
column(6,
numericInput("ms_lngvtbc","Lung Tissue to Total Lung Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "lung_blood",
fluidRow(
column(6,
numericInput("ms_vlngc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0144, step = 0.01)),
column(6,
numericInput("ms_qlngc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.0234))
)
),
tabItem(
tabName = "heart_tissue",
fluidRow(
column(6,
numericInput("ms_hrtvtbc","Heart Tissue to Total Heart Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "heart_blood",
fluidRow(
column(6,
numericInput("ms_vhrtc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0051, step = 0.01)),
column(6,
numericInput("ms_qhrtc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.10536))
)
),
tabItem(
tabName = "gi_tissue",
fluidRow(
column(6,
numericInput("ms_givtbc","GI Tissue to Total GI Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "gi_blood",
fluidRow(
column(6,
numericInput("ms_vgic","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_qgic","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.1139))
)
),
tabItem(
tabName = "liver_tissue",
fluidRow(
column(6,
numericInput("ms_livvtbc","Liver Tissue to Total Liver Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "liver_blood",
fluidRow(
column(6,
numericInput("ms_vlivc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0225, step = 0.01))
),
fluidRow(
column(6,
numericInput("ms_qalivc","Arterial Blood Flow to Liver (Fraction of Cardiac Output)",min =0 , max =1, value =0.0381)),
column(6,
numericInput("ms_qvlivc","Fraction of Venous Liver Flow",min =0 , max =1, value =0.152))
)
),
tabItem(
tabName = "kidney_tissue",
fluidRow(
column(6,
numericInput("ms_kdnvtbc","Kidney Tissue to Total Kidney Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "kidney_blood",
fluidRow(
column(6,
numericInput("ms_vkdnc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0046, step = 0.01)),
column(6,
numericInput("ms_qkdnc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.16886))
)
),
tabItem(
tabName = "rpf_tissue",
fluidRow(
column(6,
numericInput("ms_rpfvtbc","Rapidly Perfused Tissue to All Rapidly Perfused Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "rpf_blood",
fluidRow(
column(6,
numericInput("ms_vrpfc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qrpfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0))
)
),
tabItem(
tabName = "spf_tissue",
fluidRow(
column(6,
numericInput("ms_spfvtbc","Slowly Perfused Tissue to All Slowly Perfused Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "spf_blood",
fluidRow(
column(6,
numericInput("ms_vspfc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qspfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0))
)
)
)
)
####################chemical Body
chem_body <- dashboardBody(
fluidPage(id="Chemicals",
tags$h4("Chemical Parameters", class="pager-header"),
fluidRow(
column(6,
numericInput("ms_den","Density (g/L)",1,0,1500,1)),
column(6,
numericInput("ms_mw","Molecular Weight (g/mol)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_vpa","Vapor Pressure at 25 \U00B0 C (Pa)",1,0,250,0.01)),
column(6,
numericInput("ms_dkow","logKow in Skin at pH5.5",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_lkow","logKow (Octanol: Water Coefficient)",1,0,250,0.01)),
column(6,
numericInput("ms_wsol","Water Solubility (mg/L)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_res","Fraction Reabsorbed in Kidney",1,0,0,0.01)),
column(6,
numericInput("ms_fupls", label = "Fraction Unbound in Plasma", value = 1, 0, 1, 0.001))
),
fluidRow(
column(6,
numericInput("ms_frwsol", label = "Fraction Dissolved in Liquid Phase of Plasma", value = 1,
min=0,max = 1,step = 0.01)
)
)
)
)
######################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 = "Duration of Exposure per Day (h/day)", value = 1, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_breps","Number of Boluses per Day",1,0,100, 1)),
column(6,
awesomeCheckbox("ms_brep_flag","Repeat Exposure 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 Boluses per Day", value = 1, step = 0.1 )
)
)
),
tabItem(
tabName = "oralv",
fluidRow(
column(6,
numericInput("ms_bdosev",label="Daily Oral Dose (mg/kg BW)", value =0, step= 0.01)),
column(6,
numericInput("ms_blenv",label = "Duration of Exposure per Day (h/day)", value = 1, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_brepsv","Number of Boluses per Day",1,0,100, 1)),
column(6,
awesomeCheckbox("ms_brepv_flag","Repeat Exposure Daily?",value = F))
)
),
tabItem(
tabName = "inh",
fluidRow(
column(4,
numericInput("ms_inhdose",label="Inhalation Exposure (ppm)", value =0, step= 0.01)),
column(4,
numericInput("ms_inhtlen",label = "Duration of Inhalation Exposure (h/day)",8)),
column(4,
numericInput("ms_inhdays",label = "Exposure Days in a Week",7))
)
),
tabItem(
tabName = "iv",
fluidRow(
column(6,
numericInput("ms_ivdose",label = "IV Infusion (mg/h)",value = 0,step = 0.01)
),
column(6,
numericInput("ms_ivlen",label="Duration of IV Infusion (h)",0))
),
fluidRow(
column(6,
awesomeCheckbox("ms_ivrep_flag","Repeat Exposure Daily?",value = F))
)
),
tabItem(
tabName = "dermal",
fluidRow(
column(6,
numericInput("ms_dermrate","Dermal Deposition Rate (mg/cm\U00B2/h)",0,step = 0.1)),
column(6,
numericInput("ms_skarea","Exposed Surface Area (cm\U00B2)",0,step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_dermlen","Duration of Dermal Exposure per Day (h/day)",0.1,step=0.01)),
column(6,
awesomeCheckbox("ms_dermrep_flag","Repeat Exposure Daily?",value = F))
)
)
)
)
#################Shiny UI
shinyUI(fluidPage(
shinyjs::useShinyjs(),
shinyWidgets::useSweetAlert(),
theme = shinythemes::shinytheme("spacelab"),
#shinythemes::themeSelector(),
includeCSS("www/styles.css"),
shinyjs::extendShinyjs(text = jscode, functions = c("disableTab", "enableTab", "reset")),
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$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
#rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,selected = "home",
navbarMenu("File",
tabPanel(title= "New",value = "new",icon = icon("plus")),
tabPanel(title = "Load",value = "load",icon = icon("floppy-open",lib = "glyphicon" )),
hidden(tabPanel(title = "Save",value = "save",icon = icon("floppy-save",lib = "glyphicon"))),
#tabPanel( id = "help" , title= "help", value = "Help", icon = icon("info")),
tabPanel(title = "Quit",value = "stop",icon=icon("power-off")),
"----",
tabPanel("About",value = "home",icon = icon("question"),
includeHTML("www/home.html")
)
),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",value = "expo",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$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 = 7, offset = 0,
selectizeInput("sel_expo",NULL,
choices = NULL,
options= list(placeholder = "Exposure Parameter Set",
openOnFocus = T))),
column(width = 5, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_expo","btn_sverest_expo","btn_saveas_expo"),
c("Import Data","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",value = "chem",
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",value= "physio",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 7, offset = 0,
selectizeInput("sel_physio",NULL,
choices = NULL,
options= list(placeholder = "Physiological Parameter Set",
openOnFocus = T))),
column(width = 5, 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(4,
shinyBS::popify(shinyBS::bsButton("btn_use_lifecourse",
"Calculate Physiological Parameters",
style = "primary",block = TRUE),
"Lifecourse Equations",
"Lifecourse equations within PLETHEM are used to calculate blood flows, tissue volumes, respiration parameters and body weight for a given age and gender. Only works for Humans")
)
),
fluidRow(
shinyBS::bsAlert("physio_header_alert")
),
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
comp_sidebar,
comp_body
)
)
)
),
tabPanel("ADME",value = "adme",
fluidPage(
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(width = 8, offset = 0,
selectizeInput("sel_adme",NULL,
choices = NULL,
options= list(placeholder = "ADME",
openOnFocus = T))),
column(width = 4, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_sverest_adme","btn_saveas_adme"),
c("Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(3,
selectizeInput("sel_expo4adme",choices= NULL,label= NULL,
options = list(placeholder = "Select Exposure"))
),
column(3,
selectizeInput("sel_chem4adme",choices = NULL,label = NULL,
options = list(placeholder = "Select Parent"))
),
column(3,
selectizeInput("sel_metabolite4adme",choices = NULL, label=NULL,
options = list(placeholder = "Select Metabolite"))
),
column(3,
selectizeInput("sel_physio4adme",choices=NULL,label = NULL,
options = list(placeholder = "Select Physiology"))
)
),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
tabsetPanel(id = "adme_tabs",type = "pills",
tabPanel("Absorption",
fluidPage(
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
column(4,
numericInput("ms_fa","Fraction Absorbed in Gut Lumen",
value = 1, min = 0, max = 1)
),
column(4,
numericInput("ms_ka","Rate of Absorption in Gut Lumen (/h)",
value = 5,min = 0)),
column(4,
numericInput("ms_kVtoL","Tranfer Rate from Vehicle to Gut Lumen (/h)",
value = 1, min = 0)
)
),
fluidRow(
column(4,
numericInput("ms_KPtot","Total Stratum Corneum Permeation Coefficient (cm\U00B2/h)",
value = 1000,min = 0)),
column(4,
numericInput("ms_maxcap","Maximum Capacity of the Startum Corneum (mg/cm\U00B2)",
value = 1000, min =0)),
column(4,
numericInput("ms_Kevap","Evaporation Rate from Stratum Corneum",
value = 1000,min = 0))
),
fluidRow(
column(4,
numericInput("ms_pair","Plasma-Air Partition Coefficient",value = 0,min = 0))
)
)
),
tabPanel("Distribution",
fluidPage(
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
column(4,
shinyBS::tipify(
pickerInput("sel_qsar4Partition", NULL,
choices = c("QSAR Model One" = 'one',
"Unified QSAR model" = 'two')
),
"Select QSAR model for partition coefficients")
),
column(2,
shinyBS::bsButton("btn_useQSAR4Partition",
"Calculate Partition",style = "primary",
block = TRUE)
)
),
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
dashboardPage(dashboardHeader(disable = T),
dashboardSidebar(sidebarMenu(id = "dist_comps",
menuItem("Fat",
tabName = "fat",selected = T),
menuItem("Skin",
tabName = "skn"),
menuItem("Muscle",
tabName = "msc"),
menuItem("Bone",
tabName = "bne"),
menuItem("Lung",
tabName = "lng"),
menuItem("Heart",
tabName = "hrt"),
menuItem("GI",
tabName = "gi"),
menuItem("Liver",
tabName = "liv"),
menuItem("Kidney",
tabName = "kdn"),
menuItem("Rapidly Perfused Tissue",
tabName = "rpf"),
menuItem("Slowly Perfused Tissue",
tabName = "spf")
)
),
dashboardBody(tabItems(
tabItem(tabName = "fat",
fluidRow(
column(6,
numericInput("ms_pfat",label = "Fat Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pafat",label = "Fat Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "skn",
fluidRow(
column(6,
numericInput("ms_pskin",label = "Skin Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_paskin",label = "Skin Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "msc",
fluidRow(
column(6,
numericInput("ms_pmusc",label = "Muscle Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pamusc",label = "Muscle Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "bne",
fluidRow(
column(6,
numericInput("ms_pbone",label = "Bone Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pabone",label = "Bone Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "brn",
fluidRow(
column(6,
numericInput("ms_pbrn",label = "Brain Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pabrn",label = "Brain Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "lng",
fluidRow(
column(6,
numericInput("ms_plng",label = "Lung Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_palng",label = "Lung Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "hrt",
fluidRow(
column(6,
numericInput("ms_phrt",label = "Heart Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pahrt",label = "Heart Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "gi",
fluidRow(
column(6,
numericInput("ms_pgi",label = "GI Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pagi",label = "GI Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "liv",
fluidRow(
column(6,
numericInput("ms_pliv",label = "Liver Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_paliv",label = "Liver Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "kdn",
fluidRow(
column(6,
numericInput("ms_pkdn",label = "Kidney Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pakdn",label = "Kidney Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "rpf",
fluidRow(
column(6,
numericInput("ms_prpf",label = "RPF Tissue Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_parpf",label = "RPF Tissue Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "spf",
fluidRow(
column(6,
numericInput("ms_pspf",label = "SPF Tissue Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_paspf",label = "SPF Tissue Permeability Coefficient",value = 1000))
)
)
)),skin = "green"
)
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
)
)),
tabPanel("Metabolism",
fluidPage(
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(4,
bsButton("btn_metab_upload",
"Upload Age-Based Metabolism Data",
block = T)
),
column(6,
selectizeInput("sel_metabfiles",choices = NULL,label = NULL)
),
column(2,
actionBttn("btn_use_age","Apply Data"))
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
),
fluidRow(
column(6,
numericInput("ms_km","Michaelis-Menten Constant for Metabolism (μM)",1,0,250,0.01)
),
column(6,
shinyBS::bsButton("btn_ivive_chem",
"Perform IVIVE",block = F)
)
),
fluidRow(
column(6,
numericInput("ms_vmaxc",paste0("Maximum Metabolism Rate (","μmol/h/kg BW^0.75)"),1,0,250,0.01)
),
column(6,
numericInput("ms_vkm1c", label = "First Order Metabolism in Liver (L/h/kg liver)", value = 1, step = 0.01)
)
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
),
fluidRow(
column(6,
numericInput("ms_kent",label = "Rate of Metabolism in the Gut lumen", value = 5, step = 0.01)
)
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
),
fluidRow(
column(6,
numericInput("ms_kbld","First Order Metabolism in Blood",0,0.75,0.95,0.01)
)
),
fluidRow(
column(6,
numericInput("ms_fuplsmet","Fraction unbound in plasma of the metabolite",1,0,1,0.01,width = validateCssUnit("100%"))),
column(6,
numericInput("ms_vdmetc","Fractional volume of distribution for the metabolite",0.6,0,1,0.01, width = validateCssUnit("100%")))
)
)),
tabPanel("Excretion",
fluidPage(
fluidRow(
column(4,
numericInput("ms_kfec","Rate of Fecal Excretion",value = 0, min = 0))
)
))
)
)
)
),
tabPanel("Uncertainty and Variability", value = "variability",
dashboardPage(
dashboardHeader(disable = T),
dashboardSidebar(
shinydashboard::sidebarMenu(
menuItem("Chemical",
tabName = "var_chem",selected = T),
menuItem("Exposure",
tabName = "var_expo"),
menuItem("Physiological",
tabName = "var_physio"),
menuItem("ADME",
tabName = "var_adme")
)
),
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_import_varphys"),#,"btn_edit_varphys"
c("New","Import"),#,"Edit"
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_import_varchem"),#,"btn_edit_varchem"
c("New","Import"),#,"Edit"
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_import_varexpo"),#,"btn_edit_varexpo"
c("New","Import"),#,"Edit"
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("expo_var_tble"))
)
),
tabItem(tabName = "var_adme",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_adme_var",NULL,
choices = NULL,
options= list(placeholder = "ADME Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varadme","btn_import_varadme"),#,"btn_edit_varadme"
c("New","Import"),#,"Edit"
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("adme_var_tble"))
)
)
)
)
)
),
tabPanel("Biomonitoring Data",value ="biomdata",
fluidPage(
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(width = 8, offset = 0,
selectizeInput("sel_biom",NULL,
choices = NULL,
options= list(placeholder = "Biomonitoring Data",
openOnFocus = T))),
column(width = 4, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_biom"),#"btn_edit_biom",
c("New"),#"Edit",
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
# fluidRow(
# column(4, offset = 1,
# tags$h4("Tissue"),
# textOutput("biom_tissue")
# ),
# column(4, offet = 2,
# tags$h4("Chemical"),
# textOutput("biom_chem")
# )
# ),
fluidRow(
plotly::plotlyOutput("biom_hist")
)
)
),
tabPanel("Simulations",
fluidPage(
fluidRow(
tags$br()
),
fluidRow(
br(),
column(8,
selectizeInput("sel_sim",NULL,choices =NULL,
width = validateCssUnit("99%"))
),
column(4,
actionGroupButtons(c("btn_new_sim","btn_run_sim"),status = "info",#"btn_edit_sim",
labels = c("New","Run"),fullwidth = T)#"Edit",
)
),
fluidRow(
wellPanel(id= "Simulationdetails",
fluidRow(
column(8,offset =2,
tags$h4("Simulation Description"),
textOutput("sim_descrp")
)
),
fluidRow(
column(3,
tags$h4("Simulation Type"),
textOutput("sim_type")
),
column(3,
tags$h4("Simulation Start (h)"),
textOutput("sim_start")
),
column(3,
tags$h4("Simulation Duration"),
textOutput("sim_dur")
),
column(3,
tags$h4("Duration Units"),
textOutput("dur_units"))
),
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(3, offset= 6,
downloadButton("downloadModel", "Download Model",class = "btn btn-primary btn-block")
),
column(
3,
actionGroupButtons(c("btn_dlHESI"),status = "btn btn-primary btn-block",
labels = c("Download Model Report"),fullwidth = T)
)
),
tabsetPanel(id = "Modeloutput", type = "tabs",
tabPanel("Plots",value = "plots",
plot_body
),
tabPanel("Parameters",value = "params",
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("Non-compartmental Analysis", value = "nca",
fluidPage(
fluidRow(
DT::DTOutput("tble_ncavals")
)
)),
tabPanel("Distribution Plots",value = "cdfpdf",
fluidPage(
bsCollapse(id = "revdos_plts",multiple = TRUE,
open = "cdfplt",
bsCollapsePanel("Cumulative Distribution Function",value = "cdfplt",
plotlyOutput("CDF")
),
bsCollapsePanel("Probability Distribution Function", value = "pdfplt",
plotlyOutput("PDF")
)
)
)
),
tabPanel("Exposure Estimates",value = "percentile",
fluidPage(
fluidRow(
DT::DTOutput("expo_estimate" )
)
))
)
)
)
))
ScitoVation/plethem documentation built on Oct. 1, 2020, 3:37 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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 = $('#'+name);
tab.unbind('click.tab');
tab.removeClass('disabled-comp');
}
shinyjs.reset = function(){history.go(0)}
"
css <- "div .disabled-comp {
color: #aaa !important;
border-color: #a00 !important;
background-color: #a00 !important;
}"
################################exposure sidebar
expo_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="ms_expo_sidebar",
tags$div(
tipify(
actionButton("clear_expo","Reset Exposures"),
"Reset all exposure values to zero. This is needed before a new set can be created",
placement = "right")
),
menuItem("Oral", tabName = "oral", selected = TRUE),
menuItem("Drinking Water", tabName = "dw"),
menuItem("Oral Exposure with Vehicle",tabName = "oralv"),
menuItem("Inhalation", tabName = "inh"),
menuItem("Intravenous", tabName = "iv"),
menuItem("Dermal",tabName = "dermal")
))
################################compartment sidebar
comp_sidebar <- shinydashboard::dashboardSidebar(
shinydashboard::sidebarMenu(id="compsidebar",
# tags$div(shinyWidgets::radioGroupButtons("ms_org",
# label = "Select Organism",
# choices = c("Human" = "ha","Rat"="ra"),
# selected = "ha",size = "normal",
# checkIcon = list(yes = icon('ok',lib ="glyphicon")))),
menuItem(tags$h5(tags$span(style = "color:white",
"Physiological Parameters")),
tabName = "physiolocal_parameters", selected = TRUE),
tags$div(class = "comp_checkboxes",
tags$h4(tags$span(style = "color:white","Model Compartments")),
checkboxGroupInput("ms_cmplist",NULL,
selected = c("fat","skin","muscle",
"bone","brain",
"lung","heart","gi",
"liver","kidney","rpf","spf"),
choiceNames = list(tags$div(id = "fat",class = "comp_tabs",
menuItem("Fat",tabName = "fat",
icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "fat_tissue"),
menuSubItem("Compartment",
tabName = "fat_blood")
)
),
tags$div(id = "skin",class = "comp_tabs",
menuItem("Skin",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "skin_tissue"),
menuSubItem("Compartment",
tabName = "skin_blood")
)
),
tags$div(id = "muscle",class = "comp_tabs",
menuItem("Muscle",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "muscle_tissue"),
menuSubItem("Compartment",
tabName = "muscle_blood")
)
),
tags$div(id = "bone",class = "comp_tabs",
menuItem("Bone",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "bone_tissue"),
menuSubItem("Compartment",
tabName = "bone_blood")
)
),
tags$div(id = "brain",class = "comp_tabs",
menuItem("Brain",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "brain_tissue"),
menuSubItem("Compartment",
tabName = "brain_blood")
)
),
tags$div(id = "lung",class = "comp_tabs",
menuItem("Lungs",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "lung_tissue"),
menuSubItem("Compartment",
tabName = "lung_blood")
)
),
tags$div(id = "heart",class = "comp_tabs",
menuItem("Heart",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "heart_tissue"),
menuSubItem("Compartment",
tabName = "heart_blood")
)
),
tags$div(id = "gi",class = "comp_tabs",
menuItem("GI",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "gi_tissue"),
menuSubItem("Compartment",
tabName = "gi_blood")
)
),
tags$div(id = "liver",class = "comp_tabs",
menuItem("Liver",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "liver_tissue"),
menuSubItem("Compartment",
tabName = "liver_blood")
)
),
tags$div(id = "kidney",class = "comp_tabs",
menuItem("Kidney",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "kidney_tissue"),
menuSubItem("Compartment",
tabName = "kidney_blood")
)
),
tags$div(id = "rpf",class = "comp_tabs",
menuItem("Rapidly Perfused",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "rpf_tissue"),
menuSubItem("Compartment",
tabName = "rpf_blood")
)
),
tags$div(id = "spf",class = "comp_tabs",
menuItem("Slowly Perfused",icon = icon("plus",class = "pull-right"),
menuSubItem("Tissue",
tabName = "spf_tissue"),
menuSubItem("Compartment",
tabName = "spf_blood")
)
)
),
choiceValues = list("fat","skin","muscle",
"bone","brain",
"lung","heart","gi",
"liver","kidney","rpf","spf")
)
)
)
)
###############################Chemical Sidebar
chem_sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(
id="chem_sidebar",
pickerInput("qsarModelChem", "Select A QSAR Model",
choices = c("QSAR Model One" = 'one'),
#"Unified QSAR model" = 'two'),
width = "99%"),
tipify(shinyBS::bsButton("qsar4chem_props",
"Estimate Fraction Dissolved",
style = "primary"),
"Estimate fraction dissoved in liquid phase of plasma using QSAR Models."
)
)
)
###########################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",
fluidRow(
column(2,
bsButton("btnAddData","Add Dataset",block = TRUE,style = "primary")
)
),
fluidRow(
column(3,
tabsetPanel(
tabPanel("Model",value = "model",
shinyWidgets::multiInput("cplt_comp",label = tags$h4("Select Compartment"),
choices = list("Arterial Plasma"="art_bld","Venous Plasma"="ven_bld",
"Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat",
"Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn",
"Bone Total"="to_bne","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne",
"Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc",
"Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn",
"Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng",
"Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt",
"GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi",
"Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv",
"Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn",
"Rapidly Perfused Total"="to_rpf",
"Rapidly Perfused Tissue"="ti_rpf","Rapidly Perfused Exchange"="bl_rpf",
"Slowly Perfused Total"="to_spf",
"Slowly Perfused Tissue"="ti_spf","Slowly Perfused Exchange"="bl_spf",
"Parent Urinary Concentration"="urine","Metabolite Urinary Concentration"="meturine"
),
selected="art_bld"
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$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("Arterial Plasma"="art_bld",
"Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat",
"Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn",
"Bone Total"="to_bne","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne",
"Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc",
"Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn",
"Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng",
"Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt",
"GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi",
"Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv",
"Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn",
"Rapidly Perused Total"="to_rpf",
"Rapidly Perused Tissue"="ti_rpf","Rapidly Perused Exchange"="bl_rpf",
"Slowly Perused Total"="to_spf",
"Slowly Perused Tissue"="ti_spf","Slowly Perused Exchange"="bl_spf"
),
selected="art_bld"
)
#selectizeInput("aplt_data",tags$h4("Select Data Sets"),choices = c("a","b","c"))
)
),
column(9,
tabBox(width = 12,height = validateCssUnit("100%"),
tabPanel("Plot",
fluidRow(
tags$h5(class="text-center",
radioButtons("r_aplt_type",label = "Amount 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 = "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("Human" = "ha","Rat"= "ra"),
selected = "ha")
),
column(4,
selectInput("ms_gender", label = "Gender",
choices = list("Male" = "M", "Female" = "F"),
selected = "M")
),
column(4,
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_qcc","Cardiac Output (L/h)",420,1,50,0.1)),
column(4,
numericInput("ms_hct","Hematocrit Factor",0.441,0,1,0.001))
),
fluidRow(
column(6,
numericInput("ms_vbldc","Fractional Blood Compartment Volume",0.0832,0.01,1,0.01)),
column(6,
numericInput("ms_perfc","Total Fractional Perfused Tissue",1,0.75,0.95,0.01)
)
),
fluidRow(
column(4,
numericInput("ms_respr","Respiration Rate (L/h)",min =0 , max =10, value =490)),
column(4,
numericInput("ms_tv","Tidal Volume (L)",min =0 , max =10, value =0.623)),
column(4,
numericInput("ms_ds","Dead Space (L)",min =0 , max =10, value =0.154))
),
fluidRow(
column(6,
numericInput("ms_uflwc","Urinary Flow Rate (L/kg/day)",min =0 , max =1, value =0.0214)),
column(6,
numericInput("ms_gfr","Glomerular Filtration (L/h)",min =0 , max =1, value =0.08)
)
)
),
tabItem(
tabName = "fat_tissue",
fluidRow(
column(6,
numericInput("ms_fatvtbc","Fat Tissue to Total Fat Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "fat_blood",
fluidRow(
column(6,
numericInput("ms_vfatc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.1841, step = 0.01)),
column(6,
numericInput("ms_qfatc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.08226))
)
),
tabItem(
tabName = "skin_tissue",
fluidRow(
column(6,
numericInput("ms_skinvtbc","Skin Tissue to Total Skin Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "skin_blood",
fluidRow(
column(6,
numericInput("ms_vskinc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0553, step = 0.01)),
column(6,
numericInput("ms_qskinc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.06783))
)
),
tabItem(
tabName = "muscle_tissue",
fluidRow(
column(6,
numericInput("ms_muscvtbc","Muscle Tissue to Total Muscle Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "muscle_blood",
fluidRow(
column(6,
numericInput("ms_vmuscc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.4576, step = 0.01)),
column(6,
numericInput("ms_qmuscc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.13711))
)
),
tabItem(
tabName = "bone_tissue",
fluidRow(
column(6,
numericInput("ms_bonevtbc","Bone Tissue to Total Bone Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "bone_blood",
fluidRow(
column(6,
numericInput("ms_vbonec","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.1318, step = 0.01)),
column(6,
numericInput("ms_qbonec","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.1266))
)
),
tabItem(
tabName = "brain_tissue",
fluidRow(
column(6,
numericInput("ms_brnvtbc","Brain Tissue to Total Brain Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "brain_blood",
fluidRow(
column(6,
numericInput("ms_vbrnc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0192, step = 0.01)),
column(6,
numericInput("ms_qbrnc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.098))
)
),
tabItem(
tabName = "lung_tissue",
fluidRow(
column(6,
numericInput("ms_lngvtbc","Lung Tissue to Total Lung Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "lung_blood",
fluidRow(
column(6,
numericInput("ms_vlngc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0144, step = 0.01)),
column(6,
numericInput("ms_qlngc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.0234))
)
),
tabItem(
tabName = "heart_tissue",
fluidRow(
column(6,
numericInput("ms_hrtvtbc","Heart Tissue to Total Heart Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "heart_blood",
fluidRow(
column(6,
numericInput("ms_vhrtc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0051, step = 0.01)),
column(6,
numericInput("ms_qhrtc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.10536))
)
),
tabItem(
tabName = "gi_tissue",
fluidRow(
column(6,
numericInput("ms_givtbc","GI Tissue to Total GI Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "gi_blood",
fluidRow(
column(6,
numericInput("ms_vgic","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_qgic","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.1139))
)
),
tabItem(
tabName = "liver_tissue",
fluidRow(
column(6,
numericInput("ms_livvtbc","Liver Tissue to Total Liver Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "liver_blood",
fluidRow(
column(6,
numericInput("ms_vlivc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0225, step = 0.01))
),
fluidRow(
column(6,
numericInput("ms_qalivc","Arterial Blood Flow to Liver (Fraction of Cardiac Output)",min =0 , max =1, value =0.0381)),
column(6,
numericInput("ms_qvlivc","Fraction of Venous Liver Flow",min =0 , max =1, value =0.152))
)
),
tabItem(
tabName = "kidney_tissue",
fluidRow(
column(6,
numericInput("ms_kdnvtbc","Kidney Tissue to Total Kidney Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "kidney_blood",
fluidRow(
column(6,
numericInput("ms_vkdnc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.0046, step = 0.01)),
column(6,
numericInput("ms_qkdnc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0.16886))
)
),
tabItem(
tabName = "rpf_tissue",
fluidRow(
column(6,
numericInput("ms_rpfvtbc","Rapidly Perfused Tissue to All Rapidly Perfused Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "rpf_blood",
fluidRow(
column(6,
numericInput("ms_vrpfc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qrpfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0))
)
),
tabItem(
tabName = "spf_tissue",
fluidRow(
column(6,
numericInput("ms_spfvtbc","Slowly Perfused Tissue to All Slowly Perfused Volume Ratio",0.95,0,1,0.01))
)
),
tabItem(
tabName = "spf_blood",
fluidRow(
column(6,
numericInput("ms_vspfc","Volume (Fraction of Body Weight)",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qspfc","Blood Flow (Fraction of Cardiac Output)",min =0 , max =1, value =0))
)
)
)
)
####################chemical Body
chem_body <- dashboardBody(
fluidPage(id="Chemicals",
tags$h4("Chemical Parameters", class="pager-header"),
fluidRow(
column(6,
numericInput("ms_den","Density (g/L)",1,0,1500,1)),
column(6,
numericInput("ms_mw","Molecular Weight (g/mol)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_vpa","Vapor Pressure at 25 \U00B0 C (Pa)",1,0,250,0.01)),
column(6,
numericInput("ms_dkow","logKow in Skin at pH5.5",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_lkow","logKow (Octanol: Water Coefficient)",1,0,250,0.01)),
column(6,
numericInput("ms_wsol","Water Solubility (mg/L)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_res","Fraction Reabsorbed in Kidney",1,0,0,0.01)),
column(6,
numericInput("ms_fupls", label = "Fraction Unbound in Plasma", value = 1, 0, 1, 0.001))
),
fluidRow(
column(6,
numericInput("ms_frwsol", label = "Fraction Dissolved in Liquid Phase of Plasma", value = 1,
min=0,max = 1,step = 0.01)
)
)
)
)
######################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 = "Duration of Exposure per Day (h/day)", value = 1, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_breps","Number of Boluses per Day",1,0,100, 1)),
column(6,
awesomeCheckbox("ms_brep_flag","Repeat Exposure 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 Boluses per Day", value = 1, step = 0.1 )
)
)
),
tabItem(
tabName = "oralv",
fluidRow(
column(6,
numericInput("ms_bdosev",label="Daily Oral Dose (mg/kg BW)", value =0, step= 0.01)),
column(6,
numericInput("ms_blenv",label = "Duration of Exposure per Day (h/day)", value = 1, step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_brepsv","Number of Boluses per Day",1,0,100, 1)),
column(6,
awesomeCheckbox("ms_brepv_flag","Repeat Exposure Daily?",value = F))
)
),
tabItem(
tabName = "inh",
fluidRow(
column(4,
numericInput("ms_inhdose",label="Inhalation Exposure (ppm)", value =0, step= 0.01)),
column(4,
numericInput("ms_inhtlen",label = "Duration of Inhalation Exposure (h/day)",8)),
column(4,
numericInput("ms_inhdays",label = "Exposure Days in a Week",7))
)
),
tabItem(
tabName = "iv",
fluidRow(
column(6,
numericInput("ms_ivdose",label = "IV Infusion (mg/h)",value = 0,step = 0.01)
),
column(6,
numericInput("ms_ivlen",label="Duration of IV Infusion (h)",0))
),
fluidRow(
column(6,
awesomeCheckbox("ms_ivrep_flag","Repeat Exposure Daily?",value = F))
)
),
tabItem(
tabName = "dermal",
fluidRow(
column(6,
numericInput("ms_dermrate","Dermal Deposition Rate (mg/cm\U00B2/h)",0,step = 0.1)),
column(6,
numericInput("ms_skarea","Exposed Surface Area (cm\U00B2)",0,step = 0.1))
),
fluidRow(
column(6,
numericInput("ms_dermlen","Duration of Dermal Exposure per Day (h/day)",0.1,step=0.01)),
column(6,
awesomeCheckbox("ms_dermrep_flag","Repeat Exposure Daily?",value = F))
)
)
)
)
#################Shiny UI
shinyUI(fluidPage(
shinyjs::useShinyjs(),
shinyWidgets::useSweetAlert(),
theme = shinythemes::shinytheme("spacelab"),
#shinythemes::themeSelector(),
includeCSS("www/styles.css"),
shinyjs::extendShinyjs(text = jscode, functions = c("disableTab", "enableTab", "reset")),
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$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
#rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,selected = "home",
navbarMenu("File",
tabPanel(title= "New",value = "new",icon = icon("plus")),
tabPanel(title = "Load",value = "load",icon = icon("floppy-open",lib = "glyphicon" )),
hidden(tabPanel(title = "Save",value = "save",icon = icon("floppy-save",lib = "glyphicon"))),
#tabPanel( id = "help" , title= "help", value = "Help", icon = icon("info")),
tabPanel(title = "Quit",value = "stop",icon=icon("power-off")),
"----",
tabPanel("About",value = "home",icon = icon("question"),
includeHTML("www/home.html")
)
),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",value = "expo",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$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 = 7, offset = 0,
selectizeInput("sel_expo",NULL,
choices = NULL,
options= list(placeholder = "Exposure Parameter Set",
openOnFocus = T))),
column(width = 5, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_expo","btn_sverest_expo","btn_saveas_expo"),
c("Import Data","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",value = "chem",
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",value= "physio",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 7, offset = 0,
selectizeInput("sel_physio",NULL,
choices = NULL,
options= list(placeholder = "Physiological Parameter Set",
openOnFocus = T))),
column(width = 5, 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(4,
shinyBS::popify(shinyBS::bsButton("btn_use_lifecourse",
"Calculate Physiological Parameters",
style = "primary",block = TRUE),
"Lifecourse Equations",
"Lifecourse equations within PLETHEM are used to calculate blood flows, tissue volumes, respiration parameters and body weight for a given age and gender. Only works for Humans")
)
),
fluidRow(
shinyBS::bsAlert("physio_header_alert")
),
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
comp_sidebar,
comp_body
)
)
)
),
tabPanel("ADME",value = "adme",
fluidPage(
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(width = 8, offset = 0,
selectizeInput("sel_adme",NULL,
choices = NULL,
options= list(placeholder = "ADME",
openOnFocus = T))),
column(width = 4, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_sverest_adme","btn_saveas_adme"),
c("Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(3,
selectizeInput("sel_expo4adme",choices= NULL,label= NULL,
options = list(placeholder = "Select Exposure"))
),
column(3,
selectizeInput("sel_chem4adme",choices = NULL,label = NULL,
options = list(placeholder = "Select Parent"))
),
column(3,
selectizeInput("sel_metabolite4adme",choices = NULL, label=NULL,
options = list(placeholder = "Select Metabolite"))
),
column(3,
selectizeInput("sel_physio4adme",choices=NULL,label = NULL,
options = list(placeholder = "Select Physiology"))
)
),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
tabsetPanel(id = "adme_tabs",type = "pills",
tabPanel("Absorption",
fluidPage(
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
column(4,
numericInput("ms_fa","Fraction Absorbed in Gut Lumen",
value = 1, min = 0, max = 1)
),
column(4,
numericInput("ms_ka","Rate of Absorption in Gut Lumen (/h)",
value = 5,min = 0)),
column(4,
numericInput("ms_kVtoL","Tranfer Rate from Vehicle to Gut Lumen (/h)",
value = 1, min = 0)
)
),
fluidRow(
column(4,
numericInput("ms_KPtot","Total Stratum Corneum Permeation Coefficient (cm\U00B2/h)",
value = 1000,min = 0)),
column(4,
numericInput("ms_maxcap","Maximum Capacity of the Startum Corneum (mg/cm\U00B2)",
value = 1000, min =0)),
column(4,
numericInput("ms_Kevap","Evaporation Rate from Stratum Corneum",
value = 1000,min = 0))
),
fluidRow(
column(4,
numericInput("ms_pair","Plasma-Air Partition Coefficient",value = 0,min = 0))
)
)
),
tabPanel("Distribution",
fluidPage(
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
column(4,
shinyBS::tipify(
pickerInput("sel_qsar4Partition", NULL,
choices = c("QSAR Model One" = 'one',
"Unified QSAR model" = 'two')
),
"Select QSAR model for partition coefficients")
),
column(2,
shinyBS::bsButton("btn_useQSAR4Partition",
"Calculate Partition",style = "primary",
block = TRUE)
)
),
fluidRow(
column(12,
div(style = "height:5px")
)
),
fluidRow(
dashboardPage(dashboardHeader(disable = T),
dashboardSidebar(sidebarMenu(id = "dist_comps",
menuItem("Fat",
tabName = "fat",selected = T),
menuItem("Skin",
tabName = "skn"),
menuItem("Muscle",
tabName = "msc"),
menuItem("Bone",
tabName = "bne"),
menuItem("Lung",
tabName = "lng"),
menuItem("Heart",
tabName = "hrt"),
menuItem("GI",
tabName = "gi"),
menuItem("Liver",
tabName = "liv"),
menuItem("Kidney",
tabName = "kdn"),
menuItem("Rapidly Perfused Tissue",
tabName = "rpf"),
menuItem("Slowly Perfused Tissue",
tabName = "spf")
)
),
dashboardBody(tabItems(
tabItem(tabName = "fat",
fluidRow(
column(6,
numericInput("ms_pfat",label = "Fat Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pafat",label = "Fat Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "skn",
fluidRow(
column(6,
numericInput("ms_pskin",label = "Skin Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_paskin",label = "Skin Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "msc",
fluidRow(
column(6,
numericInput("ms_pmusc",label = "Muscle Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pamusc",label = "Muscle Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "bne",
fluidRow(
column(6,
numericInput("ms_pbone",label = "Bone Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pabone",label = "Bone Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "brn",
fluidRow(
column(6,
numericInput("ms_pbrn",label = "Brain Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pabrn",label = "Brain Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "lng",
fluidRow(
column(6,
numericInput("ms_plng",label = "Lung Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_palng",label = "Lung Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "hrt",
fluidRow(
column(6,
numericInput("ms_phrt",label = "Heart Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pahrt",label = "Heart Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "gi",
fluidRow(
column(6,
numericInput("ms_pgi",label = "GI Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pagi",label = "GI Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "liv",
fluidRow(
column(6,
numericInput("ms_pliv",label = "Liver Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_paliv",label = "Liver Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "kdn",
fluidRow(
column(6,
numericInput("ms_pkdn",label = "Kidney Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_pakdn",label = "Kidney Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "rpf",
fluidRow(
column(6,
numericInput("ms_prpf",label = "RPF Tissue Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_parpf",label = "RPF Tissue Permeability Coefficient",value = 1000))
)
),
tabItem(tabName = "spf",
fluidRow(
column(6,
numericInput("ms_pspf",label = "SPF Tissue Partition Coefficient",value = 0.5)
),
column(6,
numericInput("ms_paspf",label = "SPF Tissue Permeability Coefficient",value = 1000))
)
)
)),skin = "green"
)
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
)
)),
tabPanel("Metabolism",
fluidPage(
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(4,
bsButton("btn_metab_upload",
"Upload Age-Based Metabolism Data",
block = T)
),
column(6,
selectizeInput("sel_metabfiles",choices = NULL,label = NULL)
),
column(2,
actionBttn("btn_use_age","Apply Data"))
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
),
fluidRow(
column(6,
numericInput("ms_km","Michaelis-Menten Constant for Metabolism (μM)",1,0,250,0.01)
),
column(6,
shinyBS::bsButton("btn_ivive_chem",
"Perform IVIVE",block = F)
)
),
fluidRow(
column(6,
numericInput("ms_vmaxc",paste0("Maximum Metabolism Rate (","μmol/h/kg BW^0.75)"),1,0,250,0.01)
),
column(6,
numericInput("ms_vkm1c", label = "First Order Metabolism in Liver (L/h/kg liver)", value = 1, step = 0.01)
)
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
),
fluidRow(
column(6,
numericInput("ms_kent",label = "Rate of Metabolism in the Gut lumen", value = 5, step = 0.01)
)
),
fluidRow(
tags$hr(style = "border: 1px dashed black;")
),
fluidRow(
column(6,
numericInput("ms_kbld","First Order Metabolism in Blood",0,0.75,0.95,0.01)
)
),
fluidRow(
column(6,
numericInput("ms_fuplsmet","Fraction unbound in plasma of the metabolite",1,0,1,0.01,width = validateCssUnit("100%"))),
column(6,
numericInput("ms_vdmetc","Fractional volume of distribution for the metabolite",0.6,0,1,0.01, width = validateCssUnit("100%")))
)
)),
tabPanel("Excretion",
fluidPage(
fluidRow(
column(4,
numericInput("ms_kfec","Rate of Fecal Excretion",value = 0, min = 0))
)
))
)
)
)
),
tabPanel("Uncertainty and Variability", value = "variability",
dashboardPage(
dashboardHeader(disable = T),
dashboardSidebar(
shinydashboard::sidebarMenu(
menuItem("Chemical",
tabName = "var_chem",selected = T),
menuItem("Exposure",
tabName = "var_expo"),
menuItem("Physiological",
tabName = "var_physio"),
menuItem("ADME",
tabName = "var_adme")
)
),
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_import_varphys"),#,"btn_edit_varphys"
c("New","Import"),#,"Edit"
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_import_varchem"),#,"btn_edit_varchem"
c("New","Import"),#,"Edit"
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_import_varexpo"),#,"btn_edit_varexpo"
c("New","Import"),#,"Edit"
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("expo_var_tble"))
)
),
tabItem(tabName = "var_adme",
fluidRow(
column(width = 4, offset = 0,
selectizeInput("sel_adme_var",NULL,
choices = NULL,
options= list(placeholder = "ADME Parameter Set",
openOnFocus = T))),
column(width = 8, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_varadme","btn_import_varadme"),#,"btn_edit_varadme"
c("New","Import"),#,"Edit"
direction = "horizontal",
status = "info",
fullwidth = T)
)
),
fluidRow(
column(8, offset = 2,
DT::DTOutput("adme_var_tble"))
)
)
)
)
)
),
tabPanel("Biomonitoring Data",value ="biomdata",
fluidPage(
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
column(width = 8, offset = 0,
selectizeInput("sel_biom",NULL,
choices = NULL,
options= list(placeholder = "Biomonitoring Data",
openOnFocus = T))),
column(width = 4, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_new_biom"),#"btn_edit_biom",
c("New"),#"Edit",
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
# fluidRow(
# column(4, offset = 1,
# tags$h4("Tissue"),
# textOutput("biom_tissue")
# ),
# column(4, offet = 2,
# tags$h4("Chemical"),
# textOutput("biom_chem")
# )
# ),
fluidRow(
plotly::plotlyOutput("biom_hist")
)
)
),
tabPanel("Simulations",
fluidPage(
fluidRow(
tags$br()
),
fluidRow(
br(),
column(8,
selectizeInput("sel_sim",NULL,choices =NULL,
width = validateCssUnit("99%"))
),
column(4,
actionGroupButtons(c("btn_new_sim","btn_run_sim"),status = "info",#"btn_edit_sim",
labels = c("New","Run"),fullwidth = T)#"Edit",
)
),
fluidRow(
wellPanel(id= "Simulationdetails",
fluidRow(
column(8,offset =2,
tags$h4("Simulation Description"),
textOutput("sim_descrp")
)
),
fluidRow(
column(3,
tags$h4("Simulation Type"),
textOutput("sim_type")
),
column(3,
tags$h4("Simulation Start (h)"),
textOutput("sim_start")
),
column(3,
tags$h4("Simulation Duration"),
textOutput("sim_dur")
),
column(3,
tags$h4("Duration Units"),
textOutput("dur_units"))
),
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(3, offset= 6,
downloadButton("downloadModel", "Download Model",class = "btn btn-primary btn-block")
),
column(
3,
actionGroupButtons(c("btn_dlHESI"),status = "btn btn-primary btn-block",
labels = c("Download Model Report"),fullwidth = T)
)
),
tabsetPanel(id = "Modeloutput", type = "tabs",
tabPanel("Plots",value = "plots",
plot_body
),
tabPanel("Parameters",value = "params",
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("Non-compartmental Analysis", value = "nca",
fluidPage(
fluidRow(
DT::DTOutput("tble_ncavals")
)
)),
tabPanel("Distribution Plots",value = "cdfpdf",
fluidPage(
bsCollapse(id = "revdos_plts",multiple = TRUE,
open = "cdfplt",
bsCollapsePanel("Cumulative Distribution Function",value = "cdfplt",
plotlyOutput("CDF")
),
bsCollapsePanel("Probability Distribution Function", value = "pdfplt",
plotlyOutput("PDF")
)
)
)
),
tabPanel("Exposure Estimates",value = "percentile",
fluidPage(
fluidRow(
DT::DTOutput("expo_estimate" )
)
))
)
)
)
))
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