inst/rapidPBPK_pop/ui.R
In sahu27/sahu: 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("Drinking Water", tabName = "dw"),
menuItem("Inhalation", tabName = "inh"),
menuItem("Intravenous", tabName = "iv")
))
################################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",
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$h4("Select Compartment"),
choices = list("Arterial Plasma"="art_bld","Venous Plasma"="ven_bld",
"Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat",
"Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn",
"Bone Total"="to_bne","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne",
"Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc",
"Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn",
"Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng",
"Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt",
"GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi",
"Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv",
"Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn",
"Rapidly Perused Total"="to_rpf",
"Rapidly Perused Tissue"="ti_rpf","Rapidly Perused Exchange"="bl_rpf",
"Slowly Perused Total"="to_spf",
"Slowly Perused Tissue"="ti_spf","Slowly Perused Exchange"="bl_spf"
)
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$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"
)
),
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 = "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" = "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(4,
numericInput("ms_vbldc","Fractional Blood Compartment Volume",0.0832,0.01,1,0.01)),
column(4,
numericInput("ms_perfc","Total Fractional Perfused Tissue",1,0.75,0.95,0.01)
),
column(4,
numericInput("ms_kbld","First Order Metabolism in Blood",0,0.75,0.95,0.01))
),
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(4,
numericInput("ms_uflw","Urinary Flow Rate (L/kg/day)",min =0 , max =1, value =0.0214)),
column(4,
numericInput("ms_gfr","Glomerular Filteration (L/h)",min =0 , max =1, value =0.08)
),
column(4,
numericInput("ms_pair", label = "Plasma-Air Partition Coefficient", value = 1,
min = 0)
)
),
fluidRow(
column(6,
numericInput("ms_fa","Fraction Absorbed in the Gut Lumen",1)),
column(6,
numericInput("ms_ka",label = "Rate of Absorption in Gut Lumen (per hour)", value = 5, step = 0.01))
)
),
tabItem(
tabName = "fat_tissue",
fluidRow(
column(6,
numericInput("ms_pafat","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.1841, step = 0.01)),
column(6,
numericInput("ms_qfatc","Blood Flow Ratio",min =0 , max =1, value =0.08226))
),
fluidRow(class="",
column(6,
numericInput("ms_pfat","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "skin_tissue",
fluidRow(
column(6,
numericInput("ms_paskin","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0553, step = 0.01)),
column(6,
numericInput("ms_qskinc","Blood Flow Ratio",min =0 , max =1, value =0.06783))
),
fluidRow(class="",
column(6,
numericInput("ms_pskin","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "muscle_tissue",
fluidRow(
column(6,
numericInput("ms_pamusc","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.4576, step = 0.01)),
column(6,
numericInput("ms_qmuscc","Blood Flow Ratio",min =0 , max =1, value =0.13711))
),
fluidRow(class="",
column(6,
numericInput("ms_pmusc","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "bone_tissue",
fluidRow(
column(6,
numericInput("ms_pabone","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.1318, step = 0.01)),
column(6,
numericInput("ms_qbonec","Blood Flow Ratio",min =0 , max =1, value =0.1266))
),
fluidRow(class="",
column(6,
numericInput("ms_pbone","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "brain_tissue",
fluidRow(
column(6,
numericInput("ms_pabrn","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0192, step = 0.01)),
column(6,
numericInput("ms_qbrnc","Blood Flow Ratio",min =0 , max =1, value =0.098))
),
fluidRow(class="",
column(6,
numericInput("ms_pbrn","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "lung_tissue",
fluidRow(
column(6,
numericInput("ms_palng","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0144, step = 0.01)),
column(6,
numericInput("ms_qlngc","Blood Flow Ratio",min =0 , max =1, value =0.0234))
),
fluidRow(class="",
column(6,
numericInput("ms_plng","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "heart_tissue",
fluidRow(
column(6,
numericInput("ms_pahrt","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0051, step = 0.01)),
column(6,
numericInput("ms_qhrtc","Blood Flow Ratio",min =0 , max =1, value =0.10536))
),
fluidRow(class="",
column(6,
numericInput("ms_phrt","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "gi_tissue",
fluidRow(
column(6,
numericInput("ms_pagi","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_qgic","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_pgi","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "liver_tissue",
fluidRow(
column(6,
numericInput("ms_paliv","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0225, step = 0.01))
),
fluidRow(
column(6,
numericInput("ms_qalivc","Aretrial Blood Flow ratio to liver",min =0 , max =1, value =0.0381)),
column(6,
numericInput("ms_qvlivc","Fraction of Venous Liver Flow",min =0 , max =1, value =0.152))
),
fluidRow(class="",
column(6,
numericInput("ms_pliv","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "kidney_tissue",
fluidRow(
column(6,
numericInput("ms_pakdn","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0046, step = 0.01)),
column(6,
numericInput("ms_qkdnc","Blood Flow Ratio",min =0 , max =1, value =0.16886))
),
fluidRow(class="",
column(6,
numericInput("ms_pkdn","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "rpf_tissue",
fluidRow(
column(6,
numericInput("ms_parpf","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qrpfc","Blood Flow Ratio",min =0 , max =1, value =0))
),
fluidRow(class="",
column(6,
numericInput("ms_prpf","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "spf_tissue",
fluidRow(
column(6,
numericInput("ms_paspf","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qspfc","Blood Flow Ratio",min =0 , max =1, value =0))
),
fluidRow(class="",
column(6,
numericInput("ms_pspf","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,
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 (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 Resorped in Kidney",1,0,0,0.01)),
column(6,
numericInput("ms_fupls", label = "Fraction Unbound in Palsma", value = 1, 0, 1, 0.001))
),
fluidRow(
column(6,
numericInput("ms_vmaxc",paste0("Maximum Metabolism Rate (","μm/h/kg BW^0.75)"),1,0,250,0.01)),
column(6,
numericInput("ms_km","Michaelis Menton Constant for Metabolism (μM)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_vkm1c", label = "First Order metabolism in Liver (L/h/kg liver)", value = 1, step = 0.01)
),
column(6,
numericInput("ms_frwsol", label = "Fraction dissolved in water", 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 = "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),
shinyjs::inlineCSS(css),
titlePanel(title="", windowTitle = "PLETHEM rapidPBPK"),
tags$head(
tags$meta(charset="utf-8"),
tags$meta(name="viewport", content="width=device-width, initial-scale=1"),
tags$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
#rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,
tabPanel("",value = "Home",icon =icon("home"),
includeHTML("www/home.html")),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$h4("Overwrite existing Parameter Set ?")),
column(2,
bsButton("exposave_yes","Yes",block = TRUE))
)),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(2,
shinyBS::bsButton("btn_seem_upload",
"Import From SEEM Data",
block = T)),
column(2,
shinyBS::bsButton("btn_sheds_upload",
"Import SHEDS-HT results",
block = T)),
column(2,
shinyBS::bsButton("btn_batch_upload",
"Import batch exposure file",
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","btn_sverest_chem","btn_saveas_chem"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
chem_sidebar,
chem_body
)
))
),
tabPanel("Physiological",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 9, offset = 0,
selectizeInput("sel_physio",NULL,
choices = NULL,
options= list(placeholder = "Physiological Parameter Set",
openOnFocus = T))),
column(width = 3, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_physio","btn_sverest_physio","btn_saveas_physio"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(2,
shinyBS::tipify(shinyBS::bsButton("btn_use_lifecourse",
"Calculate Parameters",
style = "primary",block = TRUE),
"Use Lifecourse Equation to calcualte parameters")
),
column(4,
shinyBS::tipify(selectizeInput("sel_qsar4Partition", NULL,
choices = c("QSAR model one" = 'one',
"QSAR model two" = 'two')
),
"Select QSAR model for partition coefficients")
),
column(4,
shinyBS::tipify(selectizeInput("sel_chem4Partition",NULL,
choices ="No Chemical Added"
),
"Select Chemical for qsar model")
),
column(2,
shinyBS::bsButton("btn_useQSAR4Partition",
"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"))
)
)
)
)
)
# fluidPage(
#
# fluidRow(
# column(12,
# div(style = "height:15px")
# )
# ),
# fluidRow(tags$h5("Physiology")),
# fluidRow(
# column(width = 9, offset = 0,
# selectizeInput("sel_mc_physio",NULL,
# choices = NULL,
# options= list(placeholder = "Population Parameter Set",
# openOnFocus = T))),
# column(width = 3, offset = 0,
# shinyWidgets::actionGroupButtons(
# c("btn_import_pop","btn_sverest_pop","btn_saveas_pop"),
# c("Import","Save/Restore","Save As"),
# direction = "horizontal",
# status = "info",
# fullwidth = T
#
# ))
# ),
# fluidRow(
# pickerInput("param_names",label = "Select Parameters to assign variability",
# choices = NULL,multiple = T,
# options = list('selected-text-format' = "count > 3"))
#
# )
#
#
#
# )
),
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(4,
numericInput("sim_start","Simulation Start Time (h)",0)
),
column(4,
numericInput("sim_dur","Simulation Duration (h)",0)
),
column(4,
numericInput("mc_num","Number of Montecarlo 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= "Simulationdetails1",
fluidRow(
column(8,offset =2,
tags$h4("Simulation Description"),
textOutput("sim_descrp")
)
),
fluidRow(
column(6,
tags$h4("Simulation Start (h)"),
textOutput("sim_start")
),
column(6,
tags$h4("Simulation Duration (h)"),
textOutput("sim_dur")
)
),
fluidRow(
column(6,
tags$h4("Chemical Name"),
textOutput("sim_chem")
),
column(4,
tags$h4("Exposure Name"),
textOutput("sim_expo")
)
),
fluidRow(
column(4,
tags$h4("Age"),
textOutput("sim_age")
),
column(4,
tags$h4("Gender"),
textOutput("sim_gender")
)
),
fluidRow(
column(4,
tags$h4("Metabolism Type"),
textOutput("sim_metab_type")
),
column(4,
tags$h4("Value"),
textOutput("sim_metab_val")
),
column(4,
tags$h4("Units"),
textOutput("sim_metab_units")
)
)
)
)
))
)),
tabPanel("Model Output",icon = icon("line-chart"),value = "output",
fluidRow(
column(2,
bsButton("btnAddData","Add Dataset",block = TRUE,style = "primary")
),
column(3, offset= 6,
downloadButton("downloadModel", "Download Model",class = "btn btn-primary btn-block")
),
column(1,
shinyBS::bsButton("btnOutputIntro", "Need help?",block = TRUE,style = "info"))
),
tabsetPanel(id = "Modeloutput", type = "tabs",
tabPanel("Plots",
plot_body
),
tabPanel("Parameters",
fluidPage(
fluidRow(
box(title = "Exposure Parameters",width = 4,
DT::DTOutput("expo_params_tble")),
box(title = "All Parameters",width = 4,
DT::DTOutput("chem_params_tble")),
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"))
)
))
sahu27/sahu documentation built on May 30, 2019, 2:06 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.
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("Drinking Water", tabName = "dw"),
menuItem("Inhalation", tabName = "inh"),
menuItem("Intravenous", tabName = "iv")
))
################################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",
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$h4("Select Compartment"),
choices = list("Arterial Plasma"="art_bld","Venous Plasma"="ven_bld",
"Fat Total"="to_fat","Fat Tissue"="ti_fat","Fat Exchange"="bl_fat",
"Skin Total"="to_skn","Skin Tissue"="ti_skn","Skin Exchange"="bl_skn",
"Bone Total"="to_bne","Bone Tissue"="ti_bne","Bone Exchange"="bl_bne",
"Muscle Total"="to_musc","Muscle Tissue"="ti_musc","Muscle Exchange"="bl_musc",
"Brain Total"="to_brn","Brain Tissue"="ti_brn","Brain Exchange"="bl_brn",
"Lungs Total"="to_lng","Lungs Tissue"="ti_lng","Lungs Exchange"="bl_lng",
"Heart Total"="to_hrt","Heart Tissue"="ti_hrt","Heart Exchange"="bl_hrt",
"GI Total"="to_gi","GI Tissue"="ti_gi","GI Exchange"="bl_gi",
"Liver Total"="to_liv","Liver Tissue"="ti_liv","Liver Exchange"="bl_liv",
"Kidney Total"="to_kdn","Kidney Tissue"="ti_kdn","Kidney Exchange"="bl_kdn",
"Rapidly Perused Total"="to_rpf",
"Rapidly Perused Tissue"="ti_rpf","Rapidly Perused Exchange"="bl_rpf",
"Slowly Perused Total"="to_spf",
"Slowly Perused Tissue"="ti_spf","Slowly Perused Exchange"="bl_spf"
)
)
),
tabPanel("Dataset",value = "dataset",
shinyWidgets::pickerInput("cplt_data",multiple = F,
label = tags$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"
)
),
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 = "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" = "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(4,
numericInput("ms_vbldc","Fractional Blood Compartment Volume",0.0832,0.01,1,0.01)),
column(4,
numericInput("ms_perfc","Total Fractional Perfused Tissue",1,0.75,0.95,0.01)
),
column(4,
numericInput("ms_kbld","First Order Metabolism in Blood",0,0.75,0.95,0.01))
),
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(4,
numericInput("ms_uflw","Urinary Flow Rate (L/kg/day)",min =0 , max =1, value =0.0214)),
column(4,
numericInput("ms_gfr","Glomerular Filteration (L/h)",min =0 , max =1, value =0.08)
),
column(4,
numericInput("ms_pair", label = "Plasma-Air Partition Coefficient", value = 1,
min = 0)
)
),
fluidRow(
column(6,
numericInput("ms_fa","Fraction Absorbed in the Gut Lumen",1)),
column(6,
numericInput("ms_ka",label = "Rate of Absorption in Gut Lumen (per hour)", value = 5, step = 0.01))
)
),
tabItem(
tabName = "fat_tissue",
fluidRow(
column(6,
numericInput("ms_pafat","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.1841, step = 0.01)),
column(6,
numericInput("ms_qfatc","Blood Flow Ratio",min =0 , max =1, value =0.08226))
),
fluidRow(class="",
column(6,
numericInput("ms_pfat","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "skin_tissue",
fluidRow(
column(6,
numericInput("ms_paskin","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0553, step = 0.01)),
column(6,
numericInput("ms_qskinc","Blood Flow Ratio",min =0 , max =1, value =0.06783))
),
fluidRow(class="",
column(6,
numericInput("ms_pskin","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "muscle_tissue",
fluidRow(
column(6,
numericInput("ms_pamusc","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.4576, step = 0.01)),
column(6,
numericInput("ms_qmuscc","Blood Flow Ratio",min =0 , max =1, value =0.13711))
),
fluidRow(class="",
column(6,
numericInput("ms_pmusc","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "bone_tissue",
fluidRow(
column(6,
numericInput("ms_pabone","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.1318, step = 0.01)),
column(6,
numericInput("ms_qbonec","Blood Flow Ratio",min =0 , max =1, value =0.1266))
),
fluidRow(class="",
column(6,
numericInput("ms_pbone","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "brain_tissue",
fluidRow(
column(6,
numericInput("ms_pabrn","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0192, step = 0.01)),
column(6,
numericInput("ms_qbrnc","Blood Flow Ratio",min =0 , max =1, value =0.098))
),
fluidRow(class="",
column(6,
numericInput("ms_pbrn","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "lung_tissue",
fluidRow(
column(6,
numericInput("ms_palng","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0144, step = 0.01)),
column(6,
numericInput("ms_qlngc","Blood Flow Ratio",min =0 , max =1, value =0.0234))
),
fluidRow(class="",
column(6,
numericInput("ms_plng","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "heart_tissue",
fluidRow(
column(6,
numericInput("ms_pahrt","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0051, step = 0.01)),
column(6,
numericInput("ms_qhrtc","Blood Flow Ratio",min =0 , max =1, value =0.10536))
),
fluidRow(class="",
column(6,
numericInput("ms_phrt","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "gi_tissue",
fluidRow(
column(6,
numericInput("ms_pagi","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0222, step = 0.01)),
column(6,
numericInput("ms_qgic","Blood Flow Ratio",min =0 , max =1, value =0.1139))
),
fluidRow(class="",
column(6,
numericInput("ms_pgi","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "liver_tissue",
fluidRow(
column(6,
numericInput("ms_paliv","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0225, step = 0.01))
),
fluidRow(
column(6,
numericInput("ms_qalivc","Aretrial Blood Flow ratio to liver",min =0 , max =1, value =0.0381)),
column(6,
numericInput("ms_qvlivc","Fraction of Venous Liver Flow",min =0 , max =1, value =0.152))
),
fluidRow(class="",
column(6,
numericInput("ms_pliv","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "kidney_tissue",
fluidRow(
column(6,
numericInput("ms_pakdn","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.0046, step = 0.01)),
column(6,
numericInput("ms_qkdnc","Blood Flow Ratio",min =0 , max =1, value =0.16886))
),
fluidRow(class="",
column(6,
numericInput("ms_pkdn","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "rpf_tissue",
fluidRow(
column(6,
numericInput("ms_parpf","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qrpfc","Blood Flow Ratio",min =0 , max =1, value =0))
),
fluidRow(class="",
column(6,
numericInput("ms_prpf","Partition Coefficient",0.5,0,2, 0.01)))
),
tabItem(
tabName = "spf_tissue",
fluidRow(
column(6,
numericInput("ms_paspf","Pearmeability Area Coefficient",1000,1,1000,1)),
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 Ratio",min =0, max = 1, value =0.00001, step = 0.01)),
column(6,
numericInput("ms_qspfc","Blood Flow Ratio",min =0 , max =1, value =0))
),
fluidRow(class="",
column(6,
numericInput("ms_pspf","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,
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 (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 Resorped in Kidney",1,0,0,0.01)),
column(6,
numericInput("ms_fupls", label = "Fraction Unbound in Palsma", value = 1, 0, 1, 0.001))
),
fluidRow(
column(6,
numericInput("ms_vmaxc",paste0("Maximum Metabolism Rate (","μm/h/kg BW^0.75)"),1,0,250,0.01)),
column(6,
numericInput("ms_km","Michaelis Menton Constant for Metabolism (μM)",1,0,250,0.01))
),
fluidRow(
column(6,
numericInput("ms_vkm1c", label = "First Order metabolism in Liver (L/h/kg liver)", value = 1, step = 0.01)
),
column(6,
numericInput("ms_frwsol", label = "Fraction dissolved in water", 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 = "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),
shinyjs::inlineCSS(css),
titlePanel(title="", windowTitle = "PLETHEM rapidPBPK"),
tags$head(
tags$meta(charset="utf-8"),
tags$meta(name="viewport", content="width=device-width, initial-scale=1"),
tags$link(rel="icon", type="image/png", href="chem_32.png", sizes="32x32")
),
#rintrojs::introjsUI(),
navbarPage("", id="menu",collapsible = TRUE,
tabPanel("",value = "Home",icon =icon("home"),
includeHTML("www/home.html")),
tabPanel("Model Setup",value = "setup",
icon = icon("flask"),
fluidRow(
progressBar(id = "pb",value = 0, status = "success",striped = T)
),
tabsetPanel(id= "modelSetupTabs", type = "tabs",
tabPanel("Exposure",
fluidPage(
bsModal("modalExpoSave",title = NULL,trigger = "btn_save_expo",
fluidRow(
column(8,offset = 2,
tags$h4("Overwrite existing Parameter Set ?")),
column(2,
bsButton("exposave_yes","Yes",block = TRUE))
)),
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(2,
shinyBS::bsButton("btn_seem_upload",
"Import From SEEM Data",
block = T)),
column(2,
shinyBS::bsButton("btn_sheds_upload",
"Import SHEDS-HT results",
block = T)),
column(2,
shinyBS::bsButton("btn_batch_upload",
"Import batch exposure file",
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","btn_sverest_chem","btn_saveas_chem"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(12,
div(style = "height:10px")
)
),
fluidRow(
dashboardPage(
dashboardHeader(disable = TRUE),
chem_sidebar,
chem_body
)
))
),
tabPanel("Physiological",
fluidPage(
fluidRow(
column(12,
div(style = "height:15px")
)
),
fluidRow(
column(width = 9, offset = 0,
selectizeInput("sel_physio",NULL,
choices = NULL,
options= list(placeholder = "Physiological Parameter Set",
openOnFocus = T))),
column(width = 3, offset = 0,
shinyWidgets::actionGroupButtons(
c("btn_import_physio","btn_sverest_physio","btn_saveas_physio"),
c("Import","Save/Restore","Save As"),
direction = "horizontal",
status = "info",
fullwidth = T
))
),
fluidRow(
column(2,
shinyBS::tipify(shinyBS::bsButton("btn_use_lifecourse",
"Calculate Parameters",
style = "primary",block = TRUE),
"Use Lifecourse Equation to calcualte parameters")
),
column(4,
shinyBS::tipify(selectizeInput("sel_qsar4Partition", NULL,
choices = c("QSAR model one" = 'one',
"QSAR model two" = 'two')
),
"Select QSAR model for partition coefficients")
),
column(4,
shinyBS::tipify(selectizeInput("sel_chem4Partition",NULL,
choices ="No Chemical Added"
),
"Select Chemical for qsar model")
),
column(2,
shinyBS::bsButton("btn_useQSAR4Partition",
"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"))
)
)
)
)
)
# fluidPage(
#
# fluidRow(
# column(12,
# div(style = "height:15px")
# )
# ),
# fluidRow(tags$h5("Physiology")),
# fluidRow(
# column(width = 9, offset = 0,
# selectizeInput("sel_mc_physio",NULL,
# choices = NULL,
# options= list(placeholder = "Population Parameter Set",
# openOnFocus = T))),
# column(width = 3, offset = 0,
# shinyWidgets::actionGroupButtons(
# c("btn_import_pop","btn_sverest_pop","btn_saveas_pop"),
# c("Import","Save/Restore","Save As"),
# direction = "horizontal",
# status = "info",
# fullwidth = T
#
# ))
# ),
# fluidRow(
# pickerInput("param_names",label = "Select Parameters to assign variability",
# choices = NULL,multiple = T,
# options = list('selected-text-format' = "count > 3"))
#
# )
#
#
#
# )
),
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(4,
numericInput("sim_start","Simulation Start Time (h)",0)
),
column(4,
numericInput("sim_dur","Simulation Duration (h)",0)
),
column(4,
numericInput("mc_num","Number of Montecarlo 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= "Simulationdetails1",
fluidRow(
column(8,offset =2,
tags$h4("Simulation Description"),
textOutput("sim_descrp")
)
),
fluidRow(
column(6,
tags$h4("Simulation Start (h)"),
textOutput("sim_start")
),
column(6,
tags$h4("Simulation Duration (h)"),
textOutput("sim_dur")
)
),
fluidRow(
column(6,
tags$h4("Chemical Name"),
textOutput("sim_chem")
),
column(4,
tags$h4("Exposure Name"),
textOutput("sim_expo")
)
),
fluidRow(
column(4,
tags$h4("Age"),
textOutput("sim_age")
),
column(4,
tags$h4("Gender"),
textOutput("sim_gender")
)
),
fluidRow(
column(4,
tags$h4("Metabolism Type"),
textOutput("sim_metab_type")
),
column(4,
tags$h4("Value"),
textOutput("sim_metab_val")
),
column(4,
tags$h4("Units"),
textOutput("sim_metab_units")
)
)
)
)
))
)),
tabPanel("Model Output",icon = icon("line-chart"),value = "output",
fluidRow(
column(2,
bsButton("btnAddData","Add Dataset",block = TRUE,style = "primary")
),
column(3, offset= 6,
downloadButton("downloadModel", "Download Model",class = "btn btn-primary btn-block")
),
column(1,
shinyBS::bsButton("btnOutputIntro", "Need help?",block = TRUE,style = "info"))
),
tabsetPanel(id = "Modeloutput", type = "tabs",
tabPanel("Plots",
plot_body
),
tabPanel("Parameters",
fluidPage(
fluidRow(
box(title = "Exposure Parameters",width = 4,
DT::DTOutput("expo_params_tble")),
box(title = "All Parameters",width = 4,
DT::DTOutput("chem_params_tble")),
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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