virus/app.R
In smeister/LCE_package:
library(shiny)
library(shinysky)
library(shinydashboard)
library(LCE.Package)
library(bbmle)
library(ggplot2)
ui <- navbarPage("LCE",
navbarMenu("Matt's Functions",
tabPanel("getMPN",
fluidRow(
column(width = 2, numericInput(inputId = "data.nb", label = "Nb. of datapoints", value = 12)),
column(width = 2, numericInput(inputId = "rep.nb", label = "Nb. of replicates", value = 5)),
column(width = 2, numericInput(inputId = "dil.nb", label = "Nb. of dilutions", value = 8)),
column(width = 2, textInput(inputId = "start.conc", label = "Starting volume", value = 0.01)),
column(width = 2, numericInput(inputId = "dil.fact", label = "Dilution factor", value = 10))
),
fluidRow(
column(hotable("importData"), width = 12, offset = 0.1)
),
fluidRow(
br(),
column(actionButton(inputId = "clickMPN", label = "Calculate MPN"), width = 12, offset = 0.1),
column(p(strong("Results:")), width = 12, offset = 0.1),
column(hotable("results"), width = 12, offset = 0.1)
),
fluidRow(
br(),
column(downloadButton("savegetMPN", "Save"), width = 12)
)
),
tabPanel("getK",
fixedRow(
column(width = 4, selectInput(inputId = "biorep", label = "Number of biological replicates", choices = c(1, 2, 3))),
br(),
column(width = 4, actionButton(inputId = "clickK", label = "Calculate K"), offset = 1)
),
fluidRow(
column(width = 12,
# 1st biological replicate
conditionalPanel(condition = "input.biorep == 1 || input.biorep == 2 || input.biorep == 3",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;height:350px",
column(8,
br(),
fluidRow(
column(width = 2, numericInput(inputId = "dataA1", label = "Data nb", value = 3)),
column(width = 2, numericInput(inputId = "repA1", label = "Rep. nb", value = 5)),
column(width = 2, numericInput(inputId = "dilA1", label = "Dil. nb", value = 3)),
column(width = 2, textInput(inputId = "startA1", label = "Start [ ]", value = 0.01)),
column(width = 2, numericInput(inputId = "dilfactA1", label = "Dil. fact.", value = 10))
),
fixedRow(
box(width = 12,
div(style = 'height:60px; width:100%', hotable("getKTimeA1")),
div(style = 'overflow-y: scroll; height:190px; width:100%', hotable("getKDataA1"))
)
)
),
br(),
column(4, style = "border-radius: 10px; border-width: 2px; border-style: dotted;border-color: #000000; height: 300px",
fluidRow(
column(12, style = "height:150px;",
plotOutput(outputId = "graph1", height = "150px")
)
),
br(),
fluidRow(
column(12, align = "center",
tableOutput("getKDataA2")
)
)
)
)
)
),
br(),
# 2nd biological replicate
conditionalPanel(condition = "input.biorep == 2 || input.biorep == 3",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;height:350px",
column(8,
br(),
fluidRow(
column(width = 2, numericInput(inputId = "dataB1", label = "Data nb", value = 3)),
column(width = 2, numericInput(inputId = "repB1", label = "Rep. nb", value = 5)),
column(width = 2, numericInput(inputId = "dilB1", label = "Dil. nb", value = 3)),
column(width = 2, textInput(inputId = "startB1", label = "Start [ ]", value = 0.01)),
column(width = 2, numericInput(inputId = "dilfactB1", label = "Dil. fact.", value = 10))
),
fixedRow(
box(width = 12,
div(style = 'height:60px; width:100%', hotable("getKTimeB1")),
div(style = 'overflow-y: scroll; height:190px; width:100%', hotable("getKDataB1"))
)
)
),
br(),
column(4, style = "border-radius: 10px; border-width: 2px; border-style: dotted;border-color: #000000; height: 300px",
fluidRow(
column(12, style = "height:150px;",
plotOutput(outputId = "graph2", height = "150px")
)
),
br(),
fluidRow(
column(12, align = "center",
tableOutput("getKDataB2")
)
)
)
)
)
),
br(),
# 3rd biological replicate
conditionalPanel(condition = "input.biorep == 3",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;height:350px",
column(8,
br(),
fluidRow(
column(width = 2, numericInput(inputId = "dataC1", label = "Data nb", value = 3)),
column(width = 2, numericInput(inputId = "repC1", label = "Rep. nb", value = 5)),
column(width = 2, numericInput(inputId = "dilC1", label = "Dil. nb", value = 3)),
column(width = 2, textInput(inputId = "startC1", label = "Start [ ]", value = 0.01)),
column(width = 2, numericInput(inputId = "dilfactC1", label = "Dil. fact.", value = 10))
),
fixedRow(
box(width = 12,
div(style = 'height:60px; width:100%', hotable("getKTimeC1")),
div(style = 'overflow-y: scroll; height:190px; width:100%', hotable("getKDataC1"))
)
)
),
br(),
column(4, style = "border-radius: 10px; border-width: 2px; border-style: dotted;border-color: #000000; height: 300px",
fluidRow(
column(12, style = "height:150px;",
plotOutput(outputId = "graph3", height = "150px")
)
),
br(),
fluidRow(
column(12, align = "center",
tableOutput("getKDataC2")
)
)
)
)
)
),
br(),
conditionalPanel(condition = "input.biorep == 2 | input.biorep == 3",
fluidRow(
column(12, align = "center",
h3("Results")
)
),
fluidRow(
column(6,
plotOutput(outputId = "graph0")
),
column(6, align = "center",
tableOutput("getKData0")
)
)
)
)
)
)
),
navbarMenu("Fluence/Dose Calculation",
tabPanel("UV",
sidebarLayout(
sidebarPanel(
em("Input values:"),
br(),
numericInput(inputId = "UVtemp", label = "Temperature °C", value = 22),
numericInput(inputId = "UViodide", label = "iodide [M]", value = 1.054),
numericInput(inputId = "UVvol", label = "Volume [L]", value = 0.002),
numericInput(inputId = "UVcm2", label = "Area [cm2]", value = 4.91),
br(),
em("Initial OD values:"),
numericInput(inputId = "OD300", label = "300 nm", value = 1.1181),
numericInput(inputId = "OD352", label = "352 nm", value = 0.0245),
br(),
fluidRow(
column(6, h4("Quantum Yield:")),
column(6, h4(textOutput(outputId = "QuantumY"), style = "color:red"))
),
fluidRow(
column(6, h4("Fluence [W/m2]:")),
column(6, h4(textOutput(outputId = "UVfluence"), style = "color:red"))
)
),
mainPanel(
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000; height: 380px",
column(12,
br(),
column(3, selectInput(inputId = "UVtimes", label = "Time Unit", choices = c("Hours"=3600, "Min."=60, "Sec."=1), selected = 60)),
column(3, numericInput(inputId = "UVtimesNB", label = "Points nb", value = 9)),
br(),
column(3, actionButton(inputId = "clickUV", label = "Calculate Dose/Time"))
),
column(12,
hotable("UVtimestable"),
br(),
hotable("UVODtable"),
br(),
column(12, h4("Results in [ mWs/cm2 ] or [ mJ/cm2 ]")),
hotable("resultUV")
)
)
),
fluidRow(
plotOutput("UVplotresults")
)
)
)
),
tabPanel("Sunlight",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000; height: 580px",
fluidRow(
column(12, h3("Absolute Irradiance (Atmospheric Filter)"), align = "center")
),
fluidRow(
column(2, selectInput(inputId = "sundata", label = p(em("Select profile:")), choices = c("new lamp", "old lamp"))),
column(8, em("Sun 2000, Abet Technologies, 1000W Xenon lamp"), align = "center")
),
conditionalPanel(condition = "input.sundata == 'new lamp'",
fluidRow(
column(width = 12,
plotOutput(outputId = "sungraph2", width = "100%", height = "300px")
)
)
),
conditionalPanel(condition = "input.sundata == 'old lamp'",
fluidRow(
column(width = 12,
plotOutput(outputId = "sungraph1", width = "100%", height = "300px")
)
)
),
fluidRow(
column(width = 12, align = "center", sliderInput(inputId = "sunslider", label = NULL, min = 250, max = 950, value = c(280, 320), width = "85%")
)
),
fluidRow(
column(width = 12,
column(5, h3("Fluence [ W/m2 ] :"), offset = 1),
column(3, h3(textOutput(outputId = "sunfluence"), style = "color:red"))
)
)
)
),
br(),
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000; height: 280px",
column(12,
br(),
column(2, selectInput(inputId = "suntimes", label = "Time Unit", choices = c("Hours"=3600, "Min."=60, "Sec."=1), selected = 3600)),
column(2, numericInput(inputId = "suntimesNB", label = "Points nb", value = 8)),
br(),
column(2, actionButton(inputId = "clickSUN", label = "Calculate Dose/Time"))
),
box(width = 10,
div(style = 'overflow-y: scroll; height:60px; width:900px', hotable("suntimestable"))
),
column(12, h4("Results in [ mWs/cm2 ] or [ mJ/cm2 ]")),
box(width = 10,
div(style = 'overflow-y: scroll; height:190px; width:900px', hotable("resultsun"))
)
)
)
),
tabPanel("Free Chlorine",
# Insert Free Chlorine
h4("FC stuff")
),
tabPanel("ClO2",
# Insert ClO2
h4("ClO2 stuff")
),
tabPanel("Ozone",
# Insert Ozone
h4("Ozone stuff")
)
),
navbarMenu("Database",
tabPanel("Virus Database",
fluidRow(
column(12,
box(width = 12,
div(style = 'overflow-y: scroll; height:500px;font-size:80%', dataTableOutput(outputId = "viruses"))
)
),
column(12,
br(),
downloadButton("saveDatabase", "Download Database")
)
)
),
tabPanel("Graphs Display",
fluidPage(
fluidRow(
column(2, selectInput(inputId = "virusCT", label = "Virus CT", choices = c("Virus CT" = "CT_test"), selected = "CT_test")),
column(2, selectInput(inputId = "viruschoice", label = "According to:", choices = c("Genus" = "Genus", "Family" = "Family", "Species" = "Species", "Virus Name" = "Name", "Genome type" = "GenomeT"), selected = "Genus")),
column(3, selectInput(inputId = "virusdisinf", label = "Disinfectant", choices = c("UV" = "UV","Sunlight" = "Sunlight","Chloramine" = "Chloramine", "Chlorine" = "Chlorine", "Chlorine dioxide" = "Chlorine dioxide", "Ozone" = "Ozone"), selected = "UV")),
column(3, selectInput(inputId = "viruslog", label = "Log inactivation", choices = c("2-log"=99, "3-log"=99.9, "4-log"=99.99), selected = 99)),
column(2, numericInput(inputId = "CTth", label = "CT threslhold", value = 10))
),
fluidRow(
plotOutput(outputId = "VirusGraph", width = "100%", height = "500px")
),
fluidRow(
column(width = 12, align = "center", sliderInput(inputId = "tempslider", label = "Temperature range", min = 0, max = 40, value = c(0, 40), width = "85%"))
)
)
)
)
)
##########
# SERVER #
##########
server <- function (input, output) {
###################################################
#################### getMPN #######################
# Render: Create the data table
output$importData <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$start.conc), input$dil.nb, input$dil.fact), rep.=rep(input$rep.nb, input$dil.nb))
data.frame(df, matrix("", ncol = input$data.nb, nrow = input$dil.nb))
}, readOnly = FALSE)
# Observe
observeEvent(input$clickMPN, {
df <- hot.to.df(input$importData)
output$results <- renderHotable({
calcMPN(df)
})
})
# Save Data
output$savegetMPN <- downloadHandler(
filename = function () {
paste("data", ".csv", sep="")
},
content = function (file) {
df <- hot.to.df(input$importData)
resultsDF <- data.frame(lapply(calcMPN(df), as.character), stringsAsFactors=FALSE)
df <- rbind(df, rep("", length(df)))
df <- rbind(df, c("RESULTS:", rep("", length(df)-1)))
df <- rbind(df, names(resultsDF))
df <- rbind(df, unlist(resultsDF[1,], use.names=FALSE), unlist(resultsDF[2,], use.names=FALSE), unlist(resultsDF[3,], use.names=FALSE))
df <- rbind(df, rep("", length(df)))
print(df)
write.table(df, file, sep=";", dec=".", row.names = FALSE)
}
)
#################### getMPN #######################
###################################################
#######################################################
#################### getK #############################
### 1st biological replicate ###
# Data table
output$getKDataA1 <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$startA1), input$dilA1, input$dilfactA1), rep.=rep(input$repA1, input$dilA1))
data.frame(df, matrix("", ncol = input$dataA1, nrow = input$dilA1))
}, readOnly = FALSE)
# Time/Dose table
output$getKTimeA1 <- renderHotable({
data.frame("[Time/Dose]", matrix("", ncol = input$dataA1))
}, readOnly = FALSE)
### 2nd biological replicate ###
# Data table
output$getKDataB1 <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$startB1), input$dilB1, input$dilfactB1), rep.=rep(input$repB1, input$dilB1))
data.frame(df, matrix("", ncol = input$dataB1, nrow = input$dilB1))
}, readOnly = FALSE)
# Time/Dose table
output$getKTimeB1 <- renderHotable({
data.frame("[Time/Dose]", matrix("", ncol = input$dataB1))
}, readOnly = FALSE)
### 3rd biological replicate ###
# Data table
output$getKDataC1 <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$startC1), input$dilC1, input$dilfactC1), rep.=rep(input$repC1, input$dilC1))
data.frame(df, matrix("", ncol = input$dataC1, nrow = input$dilC1))
}, readOnly = FALSE)
# Time/Dose table
output$getKTimeC1 <- renderHotable({
data.frame("[Time/Dose]", matrix("", ncol = input$dataC1))
}, readOnly = FALSE)
# Observe
observeEvent(input$clickK, {
dataLIST <- list(hot.to.df(input$getKDataA1), hot.to.df(input$getKDataB1), hot.to.df(input$getKDataC1))
timeLIST <- list(hot.to.df(input$getKTimeA1), hot.to.df(input$getKTimeB1), hot.to.df(input$getKTimeC1))
# Results output: k value table separated
output$getKDataA2 <- renderTable({
calcK(dataLIST, timeLIST, replicate = 1)
}, digits = 3, rownames = TRUE)
output$getKDataB2 <- renderTable({
calcK(dataLIST, timeLIST, replicate = 2)
}, digits = 3, rownames = TRUE)
output$getKDataC2 <- renderTable({
calcK(dataLIST, timeLIST, replicate = 3)
}, digits = 3, rownames = TRUE)
# Result output: graph separated
output$graph1 <- renderPlot({
calcK(dataLIST, timeLIST, replicate = 1, graph = TRUE)
})
output$graph2 <- renderPlot({
calcK(dataLIST, timeLIST, replicate = 2, graph = TRUE)
})
output$graph3 <- renderPlot({
calcK(dataLIST, timeLIST, replicate = 3, graph = TRUE)
})
# All values computing
output$getKData0 <- renderTable({
calcK(dataLIST, timeLIST)
}, digits = 3, rownames = TRUE)
output$graph0 <- renderPlot({
calcK(dataLIST, timeLIST, graph = TRUE)
})
})
# Save Data
#################### getK #############################
#######################################################
#######################################################
###################### Dose/Fluence ###################
## UV ##############
output$QuantumY <- renderText({
QY <- 0.75*(1 + 0.02*(input$UVtemp - 20.7))*(1 + 0.23*(input$UViodide - 0.557))
})
output$UVtimestable <- renderHotable({
UVtimestable <- data.frame("NA", matrix("", ncol = input$UVtimesNB))
colnames(UVtimestable)[1] <- "Time"
UVtimestable
}, readOnly = FALSE)
output$UVODtable <- renderHotable({
UVODtable <- data.frame("NA", matrix("", ncol = input$UVtimesNB))
colnames(UVODtable)[1] <- "OD"
UVODtable
}, readOnly = FALSE)
# Observe
observeEvent(input$clickUV, {
UVtimestable2 <- hot.to.df(input$UVtimestable)
UVdosetable <- hot.to.df(input$UVODtable)
UVdosetable2 <- hot.to.df(input$UVODtable)
QY <- 0.75*(1 + 0.02*(input$UVtemp - 20.7))*(1 + 0.23*(input$UViodide - 0.557))
w <-2
while (w <= length(UVdosetable[1,])) {
ODdiff <- as.numeric(as.character(UVdosetable[1,w])) - as.numeric(as.character(UVdosetable[1,2]))
UVdosetable2[1, w] <- (((ODdiff/26400)*input$UVvol*(1/QY))*472000000)/input$UVcm2
w = w+1
}
set_x <- as.numeric(as.vector(UVtimestable2[1,2:length(UVtimestable2)]))
set_y <- as.numeric(as.vector(UVdosetable2[1,2:length(UVdosetable2)]))
fitUV <- lm(set_y~set_x)
intercept <- coef(fitUV)[1] #intercept
slope <- coef(fitUV)[2] # slope
R2 <- summary(fitUV)$r.squared # R2
w <-2
while (w <= length(UVtimestable2[1,])) {
UVtimestable2[1, w] <- round(as.numeric(as.character(UVtimestable2[1, w]))*slope, digits = 3)
w = w+1
}
output$resultUV <- renderHotable({
resultsUV <- data.frame(UVtimestable2)
colnames(resultsUV)[1] <- "Dose"
resultsUV
})
output$UVplotresults <- renderPlot({
plot(set_x, set_y, xlab = "Time", ylab = "[mJ/cm2]")
abline(lm(fitUV),col="red")
legend("bottomright", legend = c(paste("Intercept =", round(intercept, digits = 3)), paste("Slope =", round(slope, digits = 3)), paste("r2 =", round(R2, digits = 3))), bty = "n")
})
# Fluence value in W/m2 * UVfluence
UVfluence <- slope*10/as.numeric(as.character(input$UVtimes))
output$UVfluence <- renderText({
UVfluence
})
})
## Sunlight ########
plotplot2 <- function (a, b) {
a
b
}
output$sungraph1 <- renderPlot({
plotplot2(par(mar=c(4, 4, 0, 1)), plot(sunlamp1$WL_nm, sunlamp1$Abs_Irradiance, type = "l", ylab = "Absolute Irradiance", xlab = "Wavelength [nm]"))
})
output$sungraph2 <- renderPlot({
plotplot2(par(mar=c(4, 4, 0, 1)), plot(sunlamp2$WL_nm, sunlamp2$Abs_Irradiance, type = "l", ylab = "Absolute Irradiance", xlab = "Wavelength [nm]"))
})
# Observe
observe({
if (input$sundata == "new lamp") {
output$sunfluence <- renderText({
((sum(sunlamp2$corr2[sunlamp2$WL_nm >= input$sunslider[1] & sunlamp2$WL_nm <= input$sunslider[2]]))/100)
})
} else {
if (input$sundata == "old lamp") {
output$sunfluence <- renderText({
((sum(sunlamp1$corr2[sunlamp1$WL_nm >= input$sunslider[1] & sunlamp1$WL_nm <= input$sunslider[2]]))/100)
})
}
}
})
# Table for fluence/dose calculation
output$suntimestable <- renderHotable({
suntimestable3 <- data.frame("NA", matrix("", ncol = input$suntimesNB))
colnames(suntimestable3)[1] <- "Time"
suntimestable3
}, readOnly = FALSE)
observeEvent(input$clickSUN, {
if (input$sundata == "new lamp") {
Fluence <- ((sum(sunlamp2$corr2[sunlamp2$WL_nm >= input$sunslider[1] & sunlamp2$WL_nm <= input$sunslider[2]]))/100)
suntimestable2 <- hot.to.df(input$suntimestable)
colnames(suntimestable2)[1] <- "Dose"
w <-2
while (w <= length(suntimestable2[1,])) {
suntimestable2[1, w] <- round(((as.numeric(as.character(suntimestable2[1,w]))*Fluence)/10)*as.numeric(as.character(input$suntimes)), digits = 3)
w = w+1
}
output$resultsun <- renderHotable({
data.frame(suntimestable2)
})
} else {
if (input$sundata == "old lamp") {
Fluence <- ((sum(sunlamp1$corr2[sunlamp1$WL_nm >= input$sunslider[1] & sunlamp1$WL_nm <= input$sunslider[2]]))/100)
suntimestable2 <- hot.to.df(input$suntimestable)
colnames(suntimestable2)[1] <- "Dose"
w <-2
while (w <= length(suntimestable2[1,])) {
suntimestable2[1, w] <- round(((as.numeric(as.character(suntimestable2[1,w]))*Fluence)/10)*as.numeric(as.character(input$suntimes)), digits = 3)
w = w+1
}
output$resultsun <- renderHotable({
data.frame(suntimestable2)
})
}
}
})
###################### Dose/Fluence ###################
#######################################################
#######################################################
##################### Virus Database ##################
## Database ########
output$viruses <- renderDataTable(
Virus_CT_list2
)
output$saveDatabase <- downloadHandler(
filename = function () {
paste("data", ".csv", sep="")
},
content <- function(file) {
write.table(Virus_CT_list2, file, sep=";", dec=".", row.names = FALSE)
}
)
## Graphs Display ######## "./virus/data/virus_CT_list2.csv"
#df_virus<-data.frame(read.csv2("./virus/data/Virus_CT_list2.csv", header = TRUE, dec = "."))
df_virus<-Virus_CT_list2
observe({
df_virus2 <- df_virus[df_virus$Disinfectant == input$virusdisinf,] # OKAY
if (input$virusdisinf == "UV" | input$virusdisinf == "Sunlight") {
df_virus3 <- df_virus2
} else {
df_virus3 <- df_virus2[df_virus2$Temp_test >= input$tempslider[1] & df_virus2$Temp_test <= input$tempslider[2], ]
}
df_virus4 <- df_virus3[df_virus3$Inactivation == input$viruslog,]
if (input$virusdisinf == "UV" | input$virusdisinf == "Sunlight") {
yLabel <- "mWs/cm2"
} else {
yLabel <- "mg*min/L"
}
output$VirusGraph <- renderPlot({
ggplot(data = df_virus4, aes_string(x = input$viruschoice, y = input$virusCT)) +
geom_boxplot() +
geom_hline(yintercept = input$CTth, color = "red", size = 2) +
theme(axis.text.x = element_text(angle = 45, size = 14, face = "bold", hjust = 1))+
labs(y = yLabel)
})
})
##################### Virus Database ##################
#######################################################
}
shinyApp(server = server, ui = ui)
smeister/LCE_package documentation built on May 8, 2019, 10:53 p.m.
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library(shiny)
library(shinysky)
library(shinydashboard)
library(LCE.Package)
library(bbmle)
library(ggplot2)
ui <- navbarPage("LCE",
navbarMenu("Matt's Functions",
tabPanel("getMPN",
fluidRow(
column(width = 2, numericInput(inputId = "data.nb", label = "Nb. of datapoints", value = 12)),
column(width = 2, numericInput(inputId = "rep.nb", label = "Nb. of replicates", value = 5)),
column(width = 2, numericInput(inputId = "dil.nb", label = "Nb. of dilutions", value = 8)),
column(width = 2, textInput(inputId = "start.conc", label = "Starting volume", value = 0.01)),
column(width = 2, numericInput(inputId = "dil.fact", label = "Dilution factor", value = 10))
),
fluidRow(
column(hotable("importData"), width = 12, offset = 0.1)
),
fluidRow(
br(),
column(actionButton(inputId = "clickMPN", label = "Calculate MPN"), width = 12, offset = 0.1),
column(p(strong("Results:")), width = 12, offset = 0.1),
column(hotable("results"), width = 12, offset = 0.1)
),
fluidRow(
br(),
column(downloadButton("savegetMPN", "Save"), width = 12)
)
),
tabPanel("getK",
fixedRow(
column(width = 4, selectInput(inputId = "biorep", label = "Number of biological replicates", choices = c(1, 2, 3))),
br(),
column(width = 4, actionButton(inputId = "clickK", label = "Calculate K"), offset = 1)
),
fluidRow(
column(width = 12,
# 1st biological replicate
conditionalPanel(condition = "input.biorep == 1 || input.biorep == 2 || input.biorep == 3",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;height:350px",
column(8,
br(),
fluidRow(
column(width = 2, numericInput(inputId = "dataA1", label = "Data nb", value = 3)),
column(width = 2, numericInput(inputId = "repA1", label = "Rep. nb", value = 5)),
column(width = 2, numericInput(inputId = "dilA1", label = "Dil. nb", value = 3)),
column(width = 2, textInput(inputId = "startA1", label = "Start [ ]", value = 0.01)),
column(width = 2, numericInput(inputId = "dilfactA1", label = "Dil. fact.", value = 10))
),
fixedRow(
box(width = 12,
div(style = 'height:60px; width:100%', hotable("getKTimeA1")),
div(style = 'overflow-y: scroll; height:190px; width:100%', hotable("getKDataA1"))
)
)
),
br(),
column(4, style = "border-radius: 10px; border-width: 2px; border-style: dotted;border-color: #000000; height: 300px",
fluidRow(
column(12, style = "height:150px;",
plotOutput(outputId = "graph1", height = "150px")
)
),
br(),
fluidRow(
column(12, align = "center",
tableOutput("getKDataA2")
)
)
)
)
)
),
br(),
# 2nd biological replicate
conditionalPanel(condition = "input.biorep == 2 || input.biorep == 3",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;height:350px",
column(8,
br(),
fluidRow(
column(width = 2, numericInput(inputId = "dataB1", label = "Data nb", value = 3)),
column(width = 2, numericInput(inputId = "repB1", label = "Rep. nb", value = 5)),
column(width = 2, numericInput(inputId = "dilB1", label = "Dil. nb", value = 3)),
column(width = 2, textInput(inputId = "startB1", label = "Start [ ]", value = 0.01)),
column(width = 2, numericInput(inputId = "dilfactB1", label = "Dil. fact.", value = 10))
),
fixedRow(
box(width = 12,
div(style = 'height:60px; width:100%', hotable("getKTimeB1")),
div(style = 'overflow-y: scroll; height:190px; width:100%', hotable("getKDataB1"))
)
)
),
br(),
column(4, style = "border-radius: 10px; border-width: 2px; border-style: dotted;border-color: #000000; height: 300px",
fluidRow(
column(12, style = "height:150px;",
plotOutput(outputId = "graph2", height = "150px")
)
),
br(),
fluidRow(
column(12, align = "center",
tableOutput("getKDataB2")
)
)
)
)
)
),
br(),
# 3rd biological replicate
conditionalPanel(condition = "input.biorep == 3",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;height:350px",
column(8,
br(),
fluidRow(
column(width = 2, numericInput(inputId = "dataC1", label = "Data nb", value = 3)),
column(width = 2, numericInput(inputId = "repC1", label = "Rep. nb", value = 5)),
column(width = 2, numericInput(inputId = "dilC1", label = "Dil. nb", value = 3)),
column(width = 2, textInput(inputId = "startC1", label = "Start [ ]", value = 0.01)),
column(width = 2, numericInput(inputId = "dilfactC1", label = "Dil. fact.", value = 10))
),
fixedRow(
box(width = 12,
div(style = 'height:60px; width:100%', hotable("getKTimeC1")),
div(style = 'overflow-y: scroll; height:190px; width:100%', hotable("getKDataC1"))
)
)
),
br(),
column(4, style = "border-radius: 10px; border-width: 2px; border-style: dotted;border-color: #000000; height: 300px",
fluidRow(
column(12, style = "height:150px;",
plotOutput(outputId = "graph3", height = "150px")
)
),
br(),
fluidRow(
column(12, align = "center",
tableOutput("getKDataC2")
)
)
)
)
)
),
br(),
conditionalPanel(condition = "input.biorep == 2 | input.biorep == 3",
fluidRow(
column(12, align = "center",
h3("Results")
)
),
fluidRow(
column(6,
plotOutput(outputId = "graph0")
),
column(6, align = "center",
tableOutput("getKData0")
)
)
)
)
)
)
),
navbarMenu("Fluence/Dose Calculation",
tabPanel("UV",
sidebarLayout(
sidebarPanel(
em("Input values:"),
br(),
numericInput(inputId = "UVtemp", label = "Temperature °C", value = 22),
numericInput(inputId = "UViodide", label = "iodide [M]", value = 1.054),
numericInput(inputId = "UVvol", label = "Volume [L]", value = 0.002),
numericInput(inputId = "UVcm2", label = "Area [cm2]", value = 4.91),
br(),
em("Initial OD values:"),
numericInput(inputId = "OD300", label = "300 nm", value = 1.1181),
numericInput(inputId = "OD352", label = "352 nm", value = 0.0245),
br(),
fluidRow(
column(6, h4("Quantum Yield:")),
column(6, h4(textOutput(outputId = "QuantumY"), style = "color:red"))
),
fluidRow(
column(6, h4("Fluence [W/m2]:")),
column(6, h4(textOutput(outputId = "UVfluence"), style = "color:red"))
)
),
mainPanel(
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000; height: 380px",
column(12,
br(),
column(3, selectInput(inputId = "UVtimes", label = "Time Unit", choices = c("Hours"=3600, "Min."=60, "Sec."=1), selected = 60)),
column(3, numericInput(inputId = "UVtimesNB", label = "Points nb", value = 9)),
br(),
column(3, actionButton(inputId = "clickUV", label = "Calculate Dose/Time"))
),
column(12,
hotable("UVtimestable"),
br(),
hotable("UVODtable"),
br(),
column(12, h4("Results in [ mWs/cm2 ] or [ mJ/cm2 ]")),
hotable("resultUV")
)
)
),
fluidRow(
plotOutput("UVplotresults")
)
)
)
),
tabPanel("Sunlight",
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000; height: 580px",
fluidRow(
column(12, h3("Absolute Irradiance (Atmospheric Filter)"), align = "center")
),
fluidRow(
column(2, selectInput(inputId = "sundata", label = p(em("Select profile:")), choices = c("new lamp", "old lamp"))),
column(8, em("Sun 2000, Abet Technologies, 1000W Xenon lamp"), align = "center")
),
conditionalPanel(condition = "input.sundata == 'new lamp'",
fluidRow(
column(width = 12,
plotOutput(outputId = "sungraph2", width = "100%", height = "300px")
)
)
),
conditionalPanel(condition = "input.sundata == 'old lamp'",
fluidRow(
column(width = 12,
plotOutput(outputId = "sungraph1", width = "100%", height = "300px")
)
)
),
fluidRow(
column(width = 12, align = "center", sliderInput(inputId = "sunslider", label = NULL, min = 250, max = 950, value = c(280, 320), width = "85%")
)
),
fluidRow(
column(width = 12,
column(5, h3("Fluence [ W/m2 ] :"), offset = 1),
column(3, h3(textOutput(outputId = "sunfluence"), style = "color:red"))
)
)
)
),
br(),
fluidRow(
column(12, style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000; height: 280px",
column(12,
br(),
column(2, selectInput(inputId = "suntimes", label = "Time Unit", choices = c("Hours"=3600, "Min."=60, "Sec."=1), selected = 3600)),
column(2, numericInput(inputId = "suntimesNB", label = "Points nb", value = 8)),
br(),
column(2, actionButton(inputId = "clickSUN", label = "Calculate Dose/Time"))
),
box(width = 10,
div(style = 'overflow-y: scroll; height:60px; width:900px', hotable("suntimestable"))
),
column(12, h4("Results in [ mWs/cm2 ] or [ mJ/cm2 ]")),
box(width = 10,
div(style = 'overflow-y: scroll; height:190px; width:900px', hotable("resultsun"))
)
)
)
),
tabPanel("Free Chlorine",
# Insert Free Chlorine
h4("FC stuff")
),
tabPanel("ClO2",
# Insert ClO2
h4("ClO2 stuff")
),
tabPanel("Ozone",
# Insert Ozone
h4("Ozone stuff")
)
),
navbarMenu("Database",
tabPanel("Virus Database",
fluidRow(
column(12,
box(width = 12,
div(style = 'overflow-y: scroll; height:500px;font-size:80%', dataTableOutput(outputId = "viruses"))
)
),
column(12,
br(),
downloadButton("saveDatabase", "Download Database")
)
)
),
tabPanel("Graphs Display",
fluidPage(
fluidRow(
column(2, selectInput(inputId = "virusCT", label = "Virus CT", choices = c("Virus CT" = "CT_test"), selected = "CT_test")),
column(2, selectInput(inputId = "viruschoice", label = "According to:", choices = c("Genus" = "Genus", "Family" = "Family", "Species" = "Species", "Virus Name" = "Name", "Genome type" = "GenomeT"), selected = "Genus")),
column(3, selectInput(inputId = "virusdisinf", label = "Disinfectant", choices = c("UV" = "UV","Sunlight" = "Sunlight","Chloramine" = "Chloramine", "Chlorine" = "Chlorine", "Chlorine dioxide" = "Chlorine dioxide", "Ozone" = "Ozone"), selected = "UV")),
column(3, selectInput(inputId = "viruslog", label = "Log inactivation", choices = c("2-log"=99, "3-log"=99.9, "4-log"=99.99), selected = 99)),
column(2, numericInput(inputId = "CTth", label = "CT threslhold", value = 10))
),
fluidRow(
plotOutput(outputId = "VirusGraph", width = "100%", height = "500px")
),
fluidRow(
column(width = 12, align = "center", sliderInput(inputId = "tempslider", label = "Temperature range", min = 0, max = 40, value = c(0, 40), width = "85%"))
)
)
)
)
)
##########
# SERVER #
##########
server <- function (input, output) {
###################################################
#################### getMPN #######################
# Render: Create the data table
output$importData <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$start.conc), input$dil.nb, input$dil.fact), rep.=rep(input$rep.nb, input$dil.nb))
data.frame(df, matrix("", ncol = input$data.nb, nrow = input$dil.nb))
}, readOnly = FALSE)
# Observe
observeEvent(input$clickMPN, {
df <- hot.to.df(input$importData)
output$results <- renderHotable({
calcMPN(df)
})
})
# Save Data
output$savegetMPN <- downloadHandler(
filename = function () {
paste("data", ".csv", sep="")
},
content = function (file) {
df <- hot.to.df(input$importData)
resultsDF <- data.frame(lapply(calcMPN(df), as.character), stringsAsFactors=FALSE)
df <- rbind(df, rep("", length(df)))
df <- rbind(df, c("RESULTS:", rep("", length(df)-1)))
df <- rbind(df, names(resultsDF))
df <- rbind(df, unlist(resultsDF[1,], use.names=FALSE), unlist(resultsDF[2,], use.names=FALSE), unlist(resultsDF[3,], use.names=FALSE))
df <- rbind(df, rep("", length(df)))
print(df)
write.table(df, file, sep=";", dec=".", row.names = FALSE)
}
)
#################### getMPN #######################
###################################################
#######################################################
#################### getK #############################
### 1st biological replicate ###
# Data table
output$getKDataA1 <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$startA1), input$dilA1, input$dilfactA1), rep.=rep(input$repA1, input$dilA1))
data.frame(df, matrix("", ncol = input$dataA1, nrow = input$dilA1))
}, readOnly = FALSE)
# Time/Dose table
output$getKTimeA1 <- renderHotable({
data.frame("[Time/Dose]", matrix("", ncol = input$dataA1))
}, readOnly = FALSE)
### 2nd biological replicate ###
# Data table
output$getKDataB1 <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$startB1), input$dilB1, input$dilfactB1), rep.=rep(input$repB1, input$dilB1))
data.frame(df, matrix("", ncol = input$dataB1, nrow = input$dilB1))
}, readOnly = FALSE)
# Time/Dose table
output$getKTimeB1 <- renderHotable({
data.frame("[Time/Dose]", matrix("", ncol = input$dataB1))
}, readOnly = FALSE)
### 3rd biological replicate ###
# Data table
output$getKDataC1 <- renderHotable({
df<-data.frame(dil.=repDIL(as.numeric(input$startC1), input$dilC1, input$dilfactC1), rep.=rep(input$repC1, input$dilC1))
data.frame(df, matrix("", ncol = input$dataC1, nrow = input$dilC1))
}, readOnly = FALSE)
# Time/Dose table
output$getKTimeC1 <- renderHotable({
data.frame("[Time/Dose]", matrix("", ncol = input$dataC1))
}, readOnly = FALSE)
# Observe
observeEvent(input$clickK, {
dataLIST <- list(hot.to.df(input$getKDataA1), hot.to.df(input$getKDataB1), hot.to.df(input$getKDataC1))
timeLIST <- list(hot.to.df(input$getKTimeA1), hot.to.df(input$getKTimeB1), hot.to.df(input$getKTimeC1))
# Results output: k value table separated
output$getKDataA2 <- renderTable({
calcK(dataLIST, timeLIST, replicate = 1)
}, digits = 3, rownames = TRUE)
output$getKDataB2 <- renderTable({
calcK(dataLIST, timeLIST, replicate = 2)
}, digits = 3, rownames = TRUE)
output$getKDataC2 <- renderTable({
calcK(dataLIST, timeLIST, replicate = 3)
}, digits = 3, rownames = TRUE)
# Result output: graph separated
output$graph1 <- renderPlot({
calcK(dataLIST, timeLIST, replicate = 1, graph = TRUE)
})
output$graph2 <- renderPlot({
calcK(dataLIST, timeLIST, replicate = 2, graph = TRUE)
})
output$graph3 <- renderPlot({
calcK(dataLIST, timeLIST, replicate = 3, graph = TRUE)
})
# All values computing
output$getKData0 <- renderTable({
calcK(dataLIST, timeLIST)
}, digits = 3, rownames = TRUE)
output$graph0 <- renderPlot({
calcK(dataLIST, timeLIST, graph = TRUE)
})
})
# Save Data
#################### getK #############################
#######################################################
#######################################################
###################### Dose/Fluence ###################
## UV ##############
output$QuantumY <- renderText({
QY <- 0.75*(1 + 0.02*(input$UVtemp - 20.7))*(1 + 0.23*(input$UViodide - 0.557))
})
output$UVtimestable <- renderHotable({
UVtimestable <- data.frame("NA", matrix("", ncol = input$UVtimesNB))
colnames(UVtimestable)[1] <- "Time"
UVtimestable
}, readOnly = FALSE)
output$UVODtable <- renderHotable({
UVODtable <- data.frame("NA", matrix("", ncol = input$UVtimesNB))
colnames(UVODtable)[1] <- "OD"
UVODtable
}, readOnly = FALSE)
# Observe
observeEvent(input$clickUV, {
UVtimestable2 <- hot.to.df(input$UVtimestable)
UVdosetable <- hot.to.df(input$UVODtable)
UVdosetable2 <- hot.to.df(input$UVODtable)
QY <- 0.75*(1 + 0.02*(input$UVtemp - 20.7))*(1 + 0.23*(input$UViodide - 0.557))
w <-2
while (w <= length(UVdosetable[1,])) {
ODdiff <- as.numeric(as.character(UVdosetable[1,w])) - as.numeric(as.character(UVdosetable[1,2]))
UVdosetable2[1, w] <- (((ODdiff/26400)*input$UVvol*(1/QY))*472000000)/input$UVcm2
w = w+1
}
set_x <- as.numeric(as.vector(UVtimestable2[1,2:length(UVtimestable2)]))
set_y <- as.numeric(as.vector(UVdosetable2[1,2:length(UVdosetable2)]))
fitUV <- lm(set_y~set_x)
intercept <- coef(fitUV)[1] #intercept
slope <- coef(fitUV)[2] # slope
R2 <- summary(fitUV)$r.squared # R2
w <-2
while (w <= length(UVtimestable2[1,])) {
UVtimestable2[1, w] <- round(as.numeric(as.character(UVtimestable2[1, w]))*slope, digits = 3)
w = w+1
}
output$resultUV <- renderHotable({
resultsUV <- data.frame(UVtimestable2)
colnames(resultsUV)[1] <- "Dose"
resultsUV
})
output$UVplotresults <- renderPlot({
plot(set_x, set_y, xlab = "Time", ylab = "[mJ/cm2]")
abline(lm(fitUV),col="red")
legend("bottomright", legend = c(paste("Intercept =", round(intercept, digits = 3)), paste("Slope =", round(slope, digits = 3)), paste("r2 =", round(R2, digits = 3))), bty = "n")
})
# Fluence value in W/m2 * UVfluence
UVfluence <- slope*10/as.numeric(as.character(input$UVtimes))
output$UVfluence <- renderText({
UVfluence
})
})
## Sunlight ########
plotplot2 <- function (a, b) {
a
b
}
output$sungraph1 <- renderPlot({
plotplot2(par(mar=c(4, 4, 0, 1)), plot(sunlamp1$WL_nm, sunlamp1$Abs_Irradiance, type = "l", ylab = "Absolute Irradiance", xlab = "Wavelength [nm]"))
})
output$sungraph2 <- renderPlot({
plotplot2(par(mar=c(4, 4, 0, 1)), plot(sunlamp2$WL_nm, sunlamp2$Abs_Irradiance, type = "l", ylab = "Absolute Irradiance", xlab = "Wavelength [nm]"))
})
# Observe
observe({
if (input$sundata == "new lamp") {
output$sunfluence <- renderText({
((sum(sunlamp2$corr2[sunlamp2$WL_nm >= input$sunslider[1] & sunlamp2$WL_nm <= input$sunslider[2]]))/100)
})
} else {
if (input$sundata == "old lamp") {
output$sunfluence <- renderText({
((sum(sunlamp1$corr2[sunlamp1$WL_nm >= input$sunslider[1] & sunlamp1$WL_nm <= input$sunslider[2]]))/100)
})
}
}
})
# Table for fluence/dose calculation
output$suntimestable <- renderHotable({
suntimestable3 <- data.frame("NA", matrix("", ncol = input$suntimesNB))
colnames(suntimestable3)[1] <- "Time"
suntimestable3
}, readOnly = FALSE)
observeEvent(input$clickSUN, {
if (input$sundata == "new lamp") {
Fluence <- ((sum(sunlamp2$corr2[sunlamp2$WL_nm >= input$sunslider[1] & sunlamp2$WL_nm <= input$sunslider[2]]))/100)
suntimestable2 <- hot.to.df(input$suntimestable)
colnames(suntimestable2)[1] <- "Dose"
w <-2
while (w <= length(suntimestable2[1,])) {
suntimestable2[1, w] <- round(((as.numeric(as.character(suntimestable2[1,w]))*Fluence)/10)*as.numeric(as.character(input$suntimes)), digits = 3)
w = w+1
}
output$resultsun <- renderHotable({
data.frame(suntimestable2)
})
} else {
if (input$sundata == "old lamp") {
Fluence <- ((sum(sunlamp1$corr2[sunlamp1$WL_nm >= input$sunslider[1] & sunlamp1$WL_nm <= input$sunslider[2]]))/100)
suntimestable2 <- hot.to.df(input$suntimestable)
colnames(suntimestable2)[1] <- "Dose"
w <-2
while (w <= length(suntimestable2[1,])) {
suntimestable2[1, w] <- round(((as.numeric(as.character(suntimestable2[1,w]))*Fluence)/10)*as.numeric(as.character(input$suntimes)), digits = 3)
w = w+1
}
output$resultsun <- renderHotable({
data.frame(suntimestable2)
})
}
}
})
###################### Dose/Fluence ###################
#######################################################
#######################################################
##################### Virus Database ##################
## Database ########
output$viruses <- renderDataTable(
Virus_CT_list2
)
output$saveDatabase <- downloadHandler(
filename = function () {
paste("data", ".csv", sep="")
},
content <- function(file) {
write.table(Virus_CT_list2, file, sep=";", dec=".", row.names = FALSE)
}
)
## Graphs Display ######## "./virus/data/virus_CT_list2.csv"
#df_virus<-data.frame(read.csv2("./virus/data/Virus_CT_list2.csv", header = TRUE, dec = "."))
df_virus<-Virus_CT_list2
observe({
df_virus2 <- df_virus[df_virus$Disinfectant == input$virusdisinf,] # OKAY
if (input$virusdisinf == "UV" | input$virusdisinf == "Sunlight") {
df_virus3 <- df_virus2
} else {
df_virus3 <- df_virus2[df_virus2$Temp_test >= input$tempslider[1] & df_virus2$Temp_test <= input$tempslider[2], ]
}
df_virus4 <- df_virus3[df_virus3$Inactivation == input$viruslog,]
if (input$virusdisinf == "UV" | input$virusdisinf == "Sunlight") {
yLabel <- "mWs/cm2"
} else {
yLabel <- "mg*min/L"
}
output$VirusGraph <- renderPlot({
ggplot(data = df_virus4, aes_string(x = input$viruschoice, y = input$virusCT)) +
geom_boxplot() +
geom_hline(yintercept = input$CTth, color = "red", size = 2) +
theme(axis.text.x = element_text(angle = 45, size = 14, face = "bold", hjust = 1))+
labs(y = yLabel)
})
})
##################### Virus Database ##################
#######################################################
}
shinyApp(server = server, ui = ui)
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