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rtf to txt, bugfix
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Franz Innerbichler
2026-05-24 17:59:47 +02:00
parent 69e3545ac7
commit e71cfd1b6a
4 changed files with 41 additions and 39 deletions
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dev/app.R
+32 -22
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@@ -100,26 +100,27 @@ server <- function(input, output, session) {
"Home",
tabPanel(
"Limit setting",
tags$style(HTML("pre { color: black; background-color: #7FAEFF55;
font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;font-size: 12px;} ")),
tags$img(src = "logo.png", class = "adv_logo"),
h4("Introduction to the bioassay software"),
# tags$mark("linear regression"), br(),
column(
3,
tags$table(
id = "dose-table",
numericInput("lEACdiffla", "lower EAC for diff. of LA", -0.175, step = 0.001),
numericInput("uEACdiffla", "upper EAC for diff. of LA", 0.189, step = 0.001),
column(3,
style = "background: #7FAEFF88",
numericInput("lEACratiola", "lower EAC ratio of LAs", 0.005, step = 0.001),
numericInput("uEACratiola", "upper EAC for ratio of LAs", 100, step = 1),
numericInput("lEACratioSlope", "lower EAC for ratio of slopes", 0.55, step = 0.01),
numericInput("uEACratioSlope", "upper EAC for ratio of slopes", 1.84, step = 0.1),
numericInput("lEACratioua", "lower EAC for ratio of UAs", 0.75, step = 0.1),
numericInput("uEACratioua", "upper EAC for ratio of UAs", 1.33, step = 0.1),
numericInput("uEACratioua", "upper EAC for ratio of UAs", 1.33, step = 0.1)),
column(3, style = "background: #7FAEFF88",
numericInput("lowerPot", "lower EAC for potency", 75, step = 1),
numericInput("upperPot", "upper EAC for potency", 133, step = 1),
numericInput("lEACratioAdiff", "lower EAC of ratio of asymptote differences", 0.75, step = 0.01),
numericInput("uEACratioAdiff", "upper EAC of ratio of asymptote differences", 1.33, step = 0.01)
)
numericInput("uEACratioAdiff", "upper EAC of ratio of asymptote differences", 1.33, step = 0.01),
numericInput("lEACdiffla", "lower EAC for diff. of LA", -0.175, step = 0.001),
numericInput("uEACdiffla", "upper EAC for diff. of LA", 0.189, step = 0.001)
)
),
tabPanel(
@@ -221,8 +222,8 @@ server <- function(input, output, session) {
column(
8,
plotOutput("XLplot"),
"Footnote: bendpoints (linear part) and asymptote points (point where asymptote is reached) are plotted in dashed and dotted lines. They indicate whether the linear part and asymptotes are catched with the current dilutions.",
"Black line is the true slope at EC50 of REF.",
htmlOutput("No4PLFitText"),
DTOutput("pottab4plXL"),
plotOutput("diagnplot"),
DTOutput("EQtests"),
@@ -278,7 +279,7 @@ server <- function(input, output, session) {
h5("F-tests on regression, significance of slopes, and preparation need to have a p-value <0.05 to pass"),
h5("All other tests pass if p-value > 0.05"),
"SST CI for difference of slopes:",
tableOutput("SlopeDiffCI"),
#tableOutput("SlopeDiffCI"),
h3("ANOVA for parallel line assay"),
DTOutput("ANOVAlin")
)
@@ -538,7 +539,8 @@ server <- function(input, output, session) {
)
})
output$sessioninfo <- renderPrint(sessionInfo())
output$pla <- renderUI({
navbarPage(
title = "pla",
@@ -612,7 +614,7 @@ server <- function(input, output, session) {
)
})
# output$sessioninfo <- renderPrint(sessioninfo())
v <- reactiveValues(num_dose = 0, next.dose.t = 0)
@@ -678,19 +680,19 @@ server <- function(input, output, session) {
Dat$Author <- input$Author
Dat$NoP <- input$NoP
Dat$Assay <- input$Assay
Dat$FITsFlag <- FALSE
#browser()
XLdat <- Dat$wb[input$sheet][[1]]
if (is.null(XLdat)) XLdat <- Dat$wb[Dat$sheets[1]][[1]]
cn <- colnames(XLdat)
logI <- grep("log", cn)
logI <- grep("log|ln", cn)
logDoseI <- grep("log_dose", cn)
if (length(logI) > 0 & length(logDoseI) == 0) {
XLdat$log_dose <- XLdat[, logI]
XLdat2 <- XLdat[, -logI]
CORro <- cor(XLdat$log_dose, XLdat[, 3])
} else if (length(logI) == 0 & length(logDoseI) == 0) {
Ind <- grep("dilu|dose|Dose|Conc|conc", cn)
Ind <- grep(".ilution|.ose|.onc", cn)
XLdat$log_dose <- log(XLdat[, Ind])
CORro <- cor(XLdat[, Ind], XLdat[, 3])
XLdat2 <- XLdat[, -Ind]
@@ -705,10 +707,10 @@ server <- function(input, output, session) {
})
output$PureErrW2 <- renderText(warning_text2())
warning_textParEst <- reactive({
warning_textPureErr <- reactive({
ifelse(PureErrFlag, "Pure Error is selected", "")
})
output$PureErrWParEst <- renderText(warning_textParEst())
output$PureErrWParEst <- renderText(warning_textPureErr())
REP$PureErr <- PureErrFlag
@@ -745,6 +747,14 @@ server <- function(input, output, session) {
pSing
})
warning_textNo4PLFit <- reactive({
ifelse(Dat$FITsFlag, "No meaningful 4PL fit was possible. This may havea several reasons: \nA control sample was tested/\n
the EC50 is not catched with the dilutions/\n the assay/reader had a problem",
"Footnote: bendpoints (linear part) and asymptote points (point where asymptote is reached) are plotted in dashed and dotted lines. They indicate whether the linear part and asymptotes are catched with the current dilutions.
Black line is the true slope at EC50 of REF.")
})
output$No4PLFitText <- renderText(warning_textNo4PLFit())
output$relpotTestTab <- renderTable({
NULL
@@ -1532,7 +1542,7 @@ server <- function(input, output, session) {
Dat$circles <- circle
REPlin$circles <- circle
sigmoid <- Dat$coeffsMUnr
if (Dat$FITsFlag) sigmoid <- NULL else sigmoid <- Dat$coeffsMUnr
pLin <- PlotLinPLA_FUNC(circle, sigmoid = sigmoid, all_l2, pl_df, indS, indT)
REPlin$pLin <- pLin
@@ -1663,7 +1673,7 @@ server <- function(input, output, session) {
as.numeric(input$lEACratiola), as.numeric(input$uEACratiola),
as.numeric(input$lEACratioSlope), as.numeric(input$uEACratioSlope),
as.numeric(input$lEACratioua), as.numeric(input$uEACratioua),
as.numeric(input$EACLinlow), as.numeric(input$EACLinupp),
as.numeric(input$EACLinlow), as.numeric(input$EACLinupp), # Limits from linear PLA page
as.numeric(input$lEACratioAdiff), as.numeric(input$uEACratioAdiff)
)