viralAPP/app.R
In smeister/viralEXP: Calculates decay rate coefficients and concentrations for experimental data from endpoint dilution assays (MPN)
library(shiny)
library(shinysky)
library(rhandsontable)
library(viralEXP)
ui <- navbarPage(title="Virus Infectivity Calculation",
tabPanel("getMPN",
fixedRow(
column(width=12,
#
"getMPN Example:"
)
),
fixedRow(
#
column(width=12,
tags$img(src='IMG for App.png', align = "center", height = "300px",width = "900px")
)
),
br(),
column(width=12,
fixedRow(style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;width:900px",
# Table 1
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 1"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb1",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb1",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb1",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import1"))
)
),
# Table 2
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 2"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb2",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb2",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb2",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import2"))
)
),
# Table 3
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 3"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb3",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb3",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb3",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import3"))
)
),
# Table 4
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 4"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb4",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb4",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb4",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import4"))
)
),
# Table 5
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 5"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb5",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb5",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb5",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import5"))
)
),
# Table 6
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 6"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb6",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb6",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb6",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import6"))
)
)
)
),
fixedRow( # MPN results (table and graph)
column(width = 12,
br(),
column(width=2, actionButton(inputId = "clickMPN", label = "Calculate MPN")),
column(width=1, downloadButton("saveMPN","Save"))
)
),
fixedRow(style="height:320px;width:950px",
column(width=12,
br(),
column(width=6,tableOutput(outputId = "table")),
column(width=6,plotOutput(outputId = "graph", height = "300px"))
)
)
),
tabPanel("getK",
#
fixedRow(
column(width=12,
#
"getK Example:"
)
),
br(),
fixedRow(
#
column(width=12,
tags$img(src='IMG for App.png', align = "center", height = "300px",width = "900px")
)
),
br(),
column(width=12,
#
fixedRow(style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;width:900px",
# table 1
column(width=4,style="padding:8px;",
fixedRow(
column(width=12,strong("Biological replicate 1"),align="center")
),
fixedRow(
column(width=12,
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kdil.nb1",label = "Dil.", value=8)),
column(width=6,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kvol.nb1",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "krep.nb1",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKDataA"))
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKTimeA"))
)
),
# Table 2
column(width=4,style="padding:8px;",
fixedRow(
column(width=12,strong("Biological replicate 2"),align="center")
),
fixedRow(
column(width=12,
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kdil.nb2",label = "Dil.", value=8)),
column(width=6,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kvol.nb2",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "krep.nb2",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKDataB"))
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKTimeB"))
)
),
# Table 3
column(width=4,style="padding:8px;",
fixedRow(
column(width=12,strong("Biological replicate 3"),align="center")
),
fixedRow(
column(width=12,
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kdil.nb3",label = "Dil.", value=8)),
column(width=6,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kvol.nb3",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "krep.nb3",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKDataC"))
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKTimeC"))
)
)
),
fixedRow( # MPN results (table and graph)
column(width = 12,
br(),
column(width=2, actionButton(inputId = "clickK", label = "Calculate K")),
column(width=1, downloadButton("saveDataK","Save"))
)
),
fixedRow(
column(width=12,
br(),
column(width=6,tableOutput(outputId = "tableK")),
column(width=6,plotOutput(outputId = "graphK", height = "300px"))
)
)
)
)
)
server <- function(input, output) {
########################################################################
########################### MPN input tables ###########################
# Table 1
output$import1 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb1)
vol.nb<-as.numeric(input$vol.nb1)
rep.nb<-as.numeric(input$rep.nb1)
df1<-data.frame(v1=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n1=as.integer(rep(rep.nb,dil.nb)),
x1=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v1", readOnly = TRUE) %>%
hot_col("n1", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35),halign="htCenter")
})
# Table 2
output$import2 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb2)
vol.nb<-as.numeric(input$vol.nb2)
rep.nb<-as.numeric(input$rep.nb2)
df1<-data.frame(v2=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n2=as.integer(rep(rep.nb,dil.nb)),
x2=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v2", readOnly = TRUE) %>%
hot_col("n2", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 3
output$import3 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb3)
vol.nb<-as.numeric(input$vol.nb3)
rep.nb<-as.numeric(input$rep.nb3)
df1<-data.frame(v3=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n3=as.integer(rep(rep.nb,dil.nb)),
x3=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v3", readOnly = TRUE) %>%
hot_col("n3", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 4
output$import4 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb4)
vol.nb<-as.numeric(input$vol.nb4)
rep.nb<-as.numeric(input$rep.nb4)
df1<-data.frame(v4=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n4=as.integer(rep(rep.nb,dil.nb)),
x4=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v4", readOnly = TRUE) %>%
hot_col("n4", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 5
output$import5 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb5)
vol.nb<-as.numeric(input$vol.nb5)
rep.nb<-as.numeric(input$rep.nb5)
df1<-data.frame(v5=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n5=as.integer(rep(rep.nb,dil.nb)),
x5=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v5", readOnly = TRUE) %>%
hot_col("n5", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 6
output$import6 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb6)
vol.nb<-as.numeric(input$vol.nb6)
rep.nb<-as.numeric(input$rep.nb6)
df1<-data.frame(v6=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n6=as.integer(rep(rep.nb,dil.nb)),
x6=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v6", readOnly = TRUE) %>%
hot_col("n6", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
########################### MPN input tables ###########################
########################################################################
########################################################################
############################ K input tables ############################
# Table K1
output$getKDataA <- renderRHandsontable({
dil.nb<-as.numeric(input$kdil.nb1)
vol.nb<-as.numeric(input$kvol.nb1)
rep.nb<-as.numeric(input$krep.nb1)
df<-data.frame(v=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n=as.integer(rep(rep.nb,dil.nb)))
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = dil.nb))
df1<-cbind(df1[1:2], lapply(df1[3:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v", readOnly = TRUE) %>%
hot_col("n", readOnly = TRUE) %>%
hot_cols(colWidths =c(65,rep(31,7)),halign="htCenter")
})
# Time/Dose table K1
output$getKTimeA <- renderRHandsontable({
df<-data.frame(Time.Dose="NA")
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = 1))
df1<-cbind(df1[1], lapply(df1[2:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("Time.Dose", readOnly = TRUE) %>%
hot_cols(colWidths =c(96,rep(31,6)),halign="htCenter")
})
# Table K2
output$getKDataB <- renderRHandsontable({
dil.nb<-as.numeric(input$kdil.nb2)
vol.nb<-as.numeric(input$kvol.nb2)
rep.nb<-as.numeric(input$krep.nb2)
df<-data.frame(v=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n=as.integer(rep(rep.nb,dil.nb)))
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = dil.nb))
df1<-cbind(df1[1:2], lapply(df1[3:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v", readOnly = TRUE) %>%
hot_col("n", readOnly = TRUE) %>%
hot_cols(colWidths =c(65,rep(31,7)),halign="htCenter")
})
# Time/Dose table K2
output$getKTimeB <- renderRHandsontable({
df<-data.frame(Time.Dose="NA")
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = 1))
df1<-cbind(df1[1], lapply(df1[2:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("Time.Dose", readOnly = TRUE) %>%
hot_cols(colWidths =c(96,rep(31,6)),halign="htCenter")
})
# Table K3
output$getKDataC <- renderRHandsontable({
dil.nb<-as.numeric(input$kdil.nb3)
vol.nb<-as.numeric(input$kvol.nb3)
rep.nb<-as.numeric(input$krep.nb3)
df<-data.frame(v=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n=as.integer(rep(rep.nb,dil.nb)))
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = dil.nb))
df1<-cbind(df1[1:2], lapply(df1[3:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v", readOnly = TRUE) %>%
hot_col("n", readOnly = TRUE) %>%
hot_cols(colWidths =c(65,rep(31,7)),halign="htCenter")
})
# Time/Dose table K3
output$getKTimeC <- renderRHandsontable({
df<-data.frame(Time.Dose="NA")
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = 1))
df1<-cbind(df1[1], lapply(df1[2:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("Time.Dose", readOnly = TRUE) %>%
hot_cols(colWidths =c(96,rep(31,6)),halign="htCenter")
})
############################ K input tables ############################
########################################################################
########################################################################
########################### MPN calculation ############################
observeEvent(input$clickMPN, {
# Table 1
df1 <- hot_to_r(input$import1)
df1$x1<-as.numeric(as.character(df1$x1))
df1$n1<-as.numeric(as.character(df1$n1))
df1$v1<-as.numeric(as.character(df1$v1))
df1<-getMPN(x=df1$x1, n=df1$n1, v=df1$v1)
# Table 2
df2 <- hot_to_r(input$import2)
df2$x2<-as.numeric(as.character(df2$x2))
df2$n2<-as.numeric(as.character(df2$n2))
df2$v2<-as.numeric(as.character(df2$v2))
df2<-getMPN(x=df2$x2, n=df2$n2, v=df2$v2)
# Table 3
df3 <- hot_to_r(input$import3)
df3$x3<-as.numeric(as.character(df3$x3))
df3$n3<-as.numeric(as.character(df3$n3))
df3$v3<-as.numeric(as.character(df3$v3))
df3<-getMPN(x=df3$x3, n=df3$n3, v=df3$v3)
# Table 4
df4 <- hot_to_r(input$import4)
df4$x4<-as.numeric(as.character(df4$x4))
df4$n4<-as.numeric(as.character(df4$n4))
df4$v4<-as.numeric(as.character(df4$v4))
df4<-getMPN(x=df4$x4, n=df4$n4, v=df4$v4)
# Table 5
df5 <- hot_to_r(input$import5)
df5$x5<-as.numeric(as.character(df5$x5))
df5$n5<-as.numeric(as.character(df5$n5))
df5$v5<-as.numeric(as.character(df5$v5))
df5<-getMPN(x=df5$x5, n=df5$n5, v=df5$v5)
# Table 6
df6 <- hot_to_r(input$import6)
df6$x6<-as.numeric(as.character(df6$x6))
df6$n6<-as.numeric(as.character(df6$n6))
df6$v6<-as.numeric(as.character(df6$v6))
df6<-getMPN(x=df6$x6, n=df6$n6, v=df6$v6)
# Final calculation
output$graph<-renderPlot({
plot(df1,df2,df3,df4,df5,df6)
})
saveData<-reactive({
plot(df1,df2,df3,df4,df5,df6, plot=FALSE)
})
output$table <- renderTable({
saveData()
})
# Save Data
thedata <- reactive(output$table)
output$saveMPN <- downloadHandler(
filename = function () {
paste("data ",Sys.Date(), ".csv", sep="")
},
content = function(file){
write.table(saveData(), file, row.names=FALSE, sep=",")
}
)
})
########################### MPN calculation ############################
########################################################################
########################################################################
############################ K calculation #############################
observeEvent(input$clickK, {
# Biological replicate 1
dfA <- hot_to_r(input$getKDataA)
timeA<-hot_to_r(input$getKTimeA)
if (any(is.na(dfA)) | any(is.na(timeA))) {
repA<-NULL
} else {
dfA1<-getMPN(x=as.numeric(as.character(dfA$X1)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA2<-getMPN(x=as.numeric(as.character(dfA$X2)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA3<-getMPN(x=as.numeric(as.character(dfA$X3)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA4<-getMPN(x=as.numeric(as.character(dfA$X4)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA5<-getMPN(x=as.numeric(as.character(dfA$X5)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA6<-getMPN(x=as.numeric(as.character(dfA$X6)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
repA<-getK(dfA1,dfA2,dfA3,dfA4,dfA5,dfA6,timeVECT=as.numeric(as.vector(timeA[1,2:length(timeA)])))
}
# Biological replicate 2
dfB <- hot_to_r(input$getKDataB)
timeB<-hot_to_r(input$getKTimeB)
if (any(is.na(dfB)) | any(is.na(timeB))) {
repB<-NULL
} else {
dfB1<-getMPN(x=as.numeric(as.character(dfB$X1)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB2<-getMPN(x=as.numeric(as.character(dfB$X2)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB3<-getMPN(x=as.numeric(as.character(dfB$X3)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB4<-getMPN(x=as.numeric(as.character(dfB$X4)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB5<-getMPN(x=as.numeric(as.character(dfB$X5)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB6<-getMPN(x=as.numeric(as.character(dfB$X6)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
repB<-getK(dfB1,dfB2,dfB3,dfB4,dfB5,dfB6,timeVECT=as.numeric(as.vector(timeB[1,2:length(timeB)])))
}
# Biological replicate 3
dfC <- hot_to_r(input$getKDataC)
timeC<-hot_to_r(input$getKTimeC)
if (any(is.na(dfC)) | any(is.na(timeC))) {
repC<-NULL
} else {
dfC1<-getMPN(x=as.numeric(as.character(dfC$X1)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC2<-getMPN(x=as.numeric(as.character(dfC$X2)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC3<-getMPN(x=as.numeric(as.character(dfC$X3)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC4<-getMPN(x=as.numeric(as.character(dfC$X4)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC5<-getMPN(x=as.numeric(as.character(dfC$X5)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC6<-getMPN(x=as.numeric(as.character(dfC$X6)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
repC<-getK(dfC1,dfC2,dfC3,dfC4,dfC5,dfC6,timeVECT=as.numeric(as.vector(timeC[1,2:length(timeC)])))
}
### getK outputs ###
# output$graphK<-renderPlot({
# plot(repA)
# })
# saveDataK<-reactive({
# print(repA)
# })
# output$tableK <- renderTable({
# saveDataK()
# })
if (is.null(c(repA,repB,repC))) {
validate(
need(input$data != "", "Please select a data set")
)
} else if (!is.null(repA) & is.null(c(repB,repC))) {
# only repA
output$graphK<-renderPlot({
plot(repA)
})
saveDataK<-reactive({
print(repA)
})
output$tableK <- renderTable({
saveDataK()
})
} else if (!is.null(c(repA,repB)) & is.null(repC)) {
# repA and repB
results<-getK(repA,repB)
output$graphK<-renderPlot({
plot(results)
})
saveDataK<-reactive({
print(results)
})
output$tableK <- renderTable({
saveDataK()
})
} else if (!is.null(c(repA,repB,repC))) {
# repA, repB and repC
results<-getK(repA,repB,repC)
output$graphK<-renderPlot({
plot(results)
})
saveDataK<-reactive({
print(results)
})
output$tableK <- renderTable({
saveDataK()
})
}
####################
})
############################ K calculation #############################
########################################################################
}
# Run the application
shinyApp(ui = ui, server = server)
smeister/viralEXP documentation built on May 29, 2019, 9:37 a.m.
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library(shiny)
library(shinysky)
library(rhandsontable)
library(viralEXP)
ui <- navbarPage(title="Virus Infectivity Calculation",
tabPanel("getMPN",
fixedRow(
column(width=12,
#
"getMPN Example:"
)
),
fixedRow(
#
column(width=12,
tags$img(src='IMG for App.png', align = "center", height = "300px",width = "900px")
)
),
br(),
column(width=12,
fixedRow(style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;width:900px",
# Table 1
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 1"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb1",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb1",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb1",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import1"))
)
),
# Table 2
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 2"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb2",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb2",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb2",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import2"))
)
),
# Table 3
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 3"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb3",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb3",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb3",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import3"))
)
),
# Table 4
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 4"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb4",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb4",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb4",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import4"))
)
),
# Table 5
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 5"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb5",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb5",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb5",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import5"))
)
),
# Table 6
column(width=2,style="padding:8px;",
fixedRow(
column(width=12,strong("Sample 6"),align="center")
),
fixedRow(
column(width=12,
column(width=4,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "dil.nb6",label = "Dil.", value = 8)),
column(width=5,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "vol.nb6",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "rep.nb6",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("import6"))
)
)
)
),
fixedRow( # MPN results (table and graph)
column(width = 12,
br(),
column(width=2, actionButton(inputId = "clickMPN", label = "Calculate MPN")),
column(width=1, downloadButton("saveMPN","Save"))
)
),
fixedRow(style="height:320px;width:950px",
column(width=12,
br(),
column(width=6,tableOutput(outputId = "table")),
column(width=6,plotOutput(outputId = "graph", height = "300px"))
)
)
),
tabPanel("getK",
#
fixedRow(
column(width=12,
#
"getK Example:"
)
),
br(),
fixedRow(
#
column(width=12,
tags$img(src='IMG for App.png', align = "center", height = "300px",width = "900px")
)
),
br(),
column(width=12,
#
fixedRow(style = "border-radius: 10px; border-width: 2px; border-style: solid;border-color: #000000;width:900px",
# table 1
column(width=4,style="padding:8px;",
fixedRow(
column(width=12,strong("Biological replicate 1"),align="center")
),
fixedRow(
column(width=12,
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kdil.nb1",label = "Dil.", value=8)),
column(width=6,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kvol.nb1",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "krep.nb1",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKDataA"))
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKTimeA"))
)
),
# Table 2
column(width=4,style="padding:8px;",
fixedRow(
column(width=12,strong("Biological replicate 2"),align="center")
),
fixedRow(
column(width=12,
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kdil.nb2",label = "Dil.", value=8)),
column(width=6,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kvol.nb2",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "krep.nb2",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKDataB"))
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKTimeB"))
)
),
# Table 3
column(width=4,style="padding:8px;",
fixedRow(
column(width=12,strong("Biological replicate 3"),align="center")
),
fixedRow(
column(width=12,
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kdil.nb3",label = "Dil.", value=8)),
column(width=6,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "kvol.nb3",label = "Vol.", value = 0.01)),
column(width=3,offset=0,style="padding:0px;text-align:center;font-size: 12px",textInput(inputId = "krep.nb3",label = "Rep.", value = 5))
)
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKDataC"))
),
fixedRow(
column(width=12,offset=0,rHandsontableOutput("getKTimeC"))
)
)
),
fixedRow( # MPN results (table and graph)
column(width = 12,
br(),
column(width=2, actionButton(inputId = "clickK", label = "Calculate K")),
column(width=1, downloadButton("saveDataK","Save"))
)
),
fixedRow(
column(width=12,
br(),
column(width=6,tableOutput(outputId = "tableK")),
column(width=6,plotOutput(outputId = "graphK", height = "300px"))
)
)
)
)
)
server <- function(input, output) {
########################################################################
########################### MPN input tables ###########################
# Table 1
output$import1 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb1)
vol.nb<-as.numeric(input$vol.nb1)
rep.nb<-as.numeric(input$rep.nb1)
df1<-data.frame(v1=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n1=as.integer(rep(rep.nb,dil.nb)),
x1=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v1", readOnly = TRUE) %>%
hot_col("n1", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35),halign="htCenter")
})
# Table 2
output$import2 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb2)
vol.nb<-as.numeric(input$vol.nb2)
rep.nb<-as.numeric(input$rep.nb2)
df1<-data.frame(v2=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n2=as.integer(rep(rep.nb,dil.nb)),
x2=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v2", readOnly = TRUE) %>%
hot_col("n2", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 3
output$import3 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb3)
vol.nb<-as.numeric(input$vol.nb3)
rep.nb<-as.numeric(input$rep.nb3)
df1<-data.frame(v3=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n3=as.integer(rep(rep.nb,dil.nb)),
x3=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v3", readOnly = TRUE) %>%
hot_col("n3", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 4
output$import4 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb4)
vol.nb<-as.numeric(input$vol.nb4)
rep.nb<-as.numeric(input$rep.nb4)
df1<-data.frame(v4=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n4=as.integer(rep(rep.nb,dil.nb)),
x4=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v4", readOnly = TRUE) %>%
hot_col("n4", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 5
output$import5 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb5)
vol.nb<-as.numeric(input$vol.nb5)
rep.nb<-as.numeric(input$rep.nb5)
df1<-data.frame(v5=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n5=as.integer(rep(rep.nb,dil.nb)),
x5=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v5", readOnly = TRUE) %>%
hot_col("n5", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
# Table 6
output$import6 <- renderRHandsontable({
dil.nb<-as.numeric(input$dil.nb6)
vol.nb<-as.numeric(input$vol.nb6)
rep.nb<-as.numeric(input$rep.nb6)
df1<-data.frame(v6=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n6=as.integer(rep(rep.nb,dil.nb)),
x6=as.integer(rep(NA,dil.nb))
)
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v6", readOnly = TRUE) %>%
hot_col("n6", readOnly = TRUE) %>%
hot_cols(colWidths =c(63,35,35), halign="htCenter")
})
########################### MPN input tables ###########################
########################################################################
########################################################################
############################ K input tables ############################
# Table K1
output$getKDataA <- renderRHandsontable({
dil.nb<-as.numeric(input$kdil.nb1)
vol.nb<-as.numeric(input$kvol.nb1)
rep.nb<-as.numeric(input$krep.nb1)
df<-data.frame(v=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n=as.integer(rep(rep.nb,dil.nb)))
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = dil.nb))
df1<-cbind(df1[1:2], lapply(df1[3:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v", readOnly = TRUE) %>%
hot_col("n", readOnly = TRUE) %>%
hot_cols(colWidths =c(65,rep(31,7)),halign="htCenter")
})
# Time/Dose table K1
output$getKTimeA <- renderRHandsontable({
df<-data.frame(Time.Dose="NA")
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = 1))
df1<-cbind(df1[1], lapply(df1[2:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("Time.Dose", readOnly = TRUE) %>%
hot_cols(colWidths =c(96,rep(31,6)),halign="htCenter")
})
# Table K2
output$getKDataB <- renderRHandsontable({
dil.nb<-as.numeric(input$kdil.nb2)
vol.nb<-as.numeric(input$kvol.nb2)
rep.nb<-as.numeric(input$krep.nb2)
df<-data.frame(v=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n=as.integer(rep(rep.nb,dil.nb)))
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = dil.nb))
df1<-cbind(df1[1:2], lapply(df1[3:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v", readOnly = TRUE) %>%
hot_col("n", readOnly = TRUE) %>%
hot_cols(colWidths =c(65,rep(31,7)),halign="htCenter")
})
# Time/Dose table K2
output$getKTimeB <- renderRHandsontable({
df<-data.frame(Time.Dose="NA")
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = 1))
df1<-cbind(df1[1], lapply(df1[2:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("Time.Dose", readOnly = TRUE) %>%
hot_cols(colWidths =c(96,rep(31,6)),halign="htCenter")
})
# Table K3
output$getKDataC <- renderRHandsontable({
dil.nb<-as.numeric(input$kdil.nb3)
vol.nb<-as.numeric(input$kvol.nb3)
rep.nb<-as.numeric(input$krep.nb3)
df<-data.frame(v=format(repDIL(vol.nb,dil.nb,10), scientific = 1),
n=as.integer(rep(rep.nb,dil.nb)))
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = dil.nb))
df1<-cbind(df1[1:2], lapply(df1[3:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("v", readOnly = TRUE) %>%
hot_col("n", readOnly = TRUE) %>%
hot_cols(colWidths =c(65,rep(31,7)),halign="htCenter")
})
# Time/Dose table K3
output$getKTimeC <- renderRHandsontable({
df<-data.frame(Time.Dose="NA")
df1<-data.frame(df, matrix(NA, ncol = 6, nrow = 1))
df1<-cbind(df1[1], lapply(df1[2:length(df1)], as.integer))
rhandsontable(df1, rowHeaders = NULL, overflow = 'visible') %>%
hot_col("Time.Dose", readOnly = TRUE) %>%
hot_cols(colWidths =c(96,rep(31,6)),halign="htCenter")
})
############################ K input tables ############################
########################################################################
########################################################################
########################### MPN calculation ############################
observeEvent(input$clickMPN, {
# Table 1
df1 <- hot_to_r(input$import1)
df1$x1<-as.numeric(as.character(df1$x1))
df1$n1<-as.numeric(as.character(df1$n1))
df1$v1<-as.numeric(as.character(df1$v1))
df1<-getMPN(x=df1$x1, n=df1$n1, v=df1$v1)
# Table 2
df2 <- hot_to_r(input$import2)
df2$x2<-as.numeric(as.character(df2$x2))
df2$n2<-as.numeric(as.character(df2$n2))
df2$v2<-as.numeric(as.character(df2$v2))
df2<-getMPN(x=df2$x2, n=df2$n2, v=df2$v2)
# Table 3
df3 <- hot_to_r(input$import3)
df3$x3<-as.numeric(as.character(df3$x3))
df3$n3<-as.numeric(as.character(df3$n3))
df3$v3<-as.numeric(as.character(df3$v3))
df3<-getMPN(x=df3$x3, n=df3$n3, v=df3$v3)
# Table 4
df4 <- hot_to_r(input$import4)
df4$x4<-as.numeric(as.character(df4$x4))
df4$n4<-as.numeric(as.character(df4$n4))
df4$v4<-as.numeric(as.character(df4$v4))
df4<-getMPN(x=df4$x4, n=df4$n4, v=df4$v4)
# Table 5
df5 <- hot_to_r(input$import5)
df5$x5<-as.numeric(as.character(df5$x5))
df5$n5<-as.numeric(as.character(df5$n5))
df5$v5<-as.numeric(as.character(df5$v5))
df5<-getMPN(x=df5$x5, n=df5$n5, v=df5$v5)
# Table 6
df6 <- hot_to_r(input$import6)
df6$x6<-as.numeric(as.character(df6$x6))
df6$n6<-as.numeric(as.character(df6$n6))
df6$v6<-as.numeric(as.character(df6$v6))
df6<-getMPN(x=df6$x6, n=df6$n6, v=df6$v6)
# Final calculation
output$graph<-renderPlot({
plot(df1,df2,df3,df4,df5,df6)
})
saveData<-reactive({
plot(df1,df2,df3,df4,df5,df6, plot=FALSE)
})
output$table <- renderTable({
saveData()
})
# Save Data
thedata <- reactive(output$table)
output$saveMPN <- downloadHandler(
filename = function () {
paste("data ",Sys.Date(), ".csv", sep="")
},
content = function(file){
write.table(saveData(), file, row.names=FALSE, sep=",")
}
)
})
########################### MPN calculation ############################
########################################################################
########################################################################
############################ K calculation #############################
observeEvent(input$clickK, {
# Biological replicate 1
dfA <- hot_to_r(input$getKDataA)
timeA<-hot_to_r(input$getKTimeA)
if (any(is.na(dfA)) | any(is.na(timeA))) {
repA<-NULL
} else {
dfA1<-getMPN(x=as.numeric(as.character(dfA$X1)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA2<-getMPN(x=as.numeric(as.character(dfA$X2)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA3<-getMPN(x=as.numeric(as.character(dfA$X3)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA4<-getMPN(x=as.numeric(as.character(dfA$X4)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA5<-getMPN(x=as.numeric(as.character(dfA$X5)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
dfA6<-getMPN(x=as.numeric(as.character(dfA$X6)), n=as.numeric(as.character(dfA$n)), v=as.numeric(as.character(dfA$v)))
repA<-getK(dfA1,dfA2,dfA3,dfA4,dfA5,dfA6,timeVECT=as.numeric(as.vector(timeA[1,2:length(timeA)])))
}
# Biological replicate 2
dfB <- hot_to_r(input$getKDataB)
timeB<-hot_to_r(input$getKTimeB)
if (any(is.na(dfB)) | any(is.na(timeB))) {
repB<-NULL
} else {
dfB1<-getMPN(x=as.numeric(as.character(dfB$X1)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB2<-getMPN(x=as.numeric(as.character(dfB$X2)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB3<-getMPN(x=as.numeric(as.character(dfB$X3)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB4<-getMPN(x=as.numeric(as.character(dfB$X4)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB5<-getMPN(x=as.numeric(as.character(dfB$X5)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
dfB6<-getMPN(x=as.numeric(as.character(dfB$X6)), n=as.numeric(as.character(dfB$n)), v=as.numeric(as.character(dfB$v)))
repB<-getK(dfB1,dfB2,dfB3,dfB4,dfB5,dfB6,timeVECT=as.numeric(as.vector(timeB[1,2:length(timeB)])))
}
# Biological replicate 3
dfC <- hot_to_r(input$getKDataC)
timeC<-hot_to_r(input$getKTimeC)
if (any(is.na(dfC)) | any(is.na(timeC))) {
repC<-NULL
} else {
dfC1<-getMPN(x=as.numeric(as.character(dfC$X1)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC2<-getMPN(x=as.numeric(as.character(dfC$X2)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC3<-getMPN(x=as.numeric(as.character(dfC$X3)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC4<-getMPN(x=as.numeric(as.character(dfC$X4)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC5<-getMPN(x=as.numeric(as.character(dfC$X5)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
dfC6<-getMPN(x=as.numeric(as.character(dfC$X6)), n=as.numeric(as.character(dfC$n)), v=as.numeric(as.character(dfC$v)))
repC<-getK(dfC1,dfC2,dfC3,dfC4,dfC5,dfC6,timeVECT=as.numeric(as.vector(timeC[1,2:length(timeC)])))
}
### getK outputs ###
# output$graphK<-renderPlot({
# plot(repA)
# })
# saveDataK<-reactive({
# print(repA)
# })
# output$tableK <- renderTable({
# saveDataK()
# })
if (is.null(c(repA,repB,repC))) {
validate(
need(input$data != "", "Please select a data set")
)
} else if (!is.null(repA) & is.null(c(repB,repC))) {
# only repA
output$graphK<-renderPlot({
plot(repA)
})
saveDataK<-reactive({
print(repA)
})
output$tableK <- renderTable({
saveDataK()
})
} else if (!is.null(c(repA,repB)) & is.null(repC)) {
# repA and repB
results<-getK(repA,repB)
output$graphK<-renderPlot({
plot(results)
})
saveDataK<-reactive({
print(results)
})
output$tableK <- renderTable({
saveDataK()
})
} else if (!is.null(c(repA,repB,repC))) {
# repA, repB and repC
results<-getK(repA,repB,repC)
output$graphK<-renderPlot({
plot(results)
})
saveDataK<-reactive({
print(results)
})
output$tableK <- renderTable({
saveDataK()
})
}
####################
})
############################ K calculation #############################
########################################################################
}
# Run the application
shinyApp(ui = ui, server = server)
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