591 lines
25 KiB
R
591 lines
25 KiB
R
|
|
||
|
|
|
||
|
|
library(shiny)
|
||
|
|
library(shinyjs)
|
||
|
|
library(shinybusy)
|
||
|
|
library(gslnls)
|
||
|
|
library(tidyverse)
|
||
|
|
library(ggplot2)
|
||
|
|
library(reshape2)
|
||
|
|
library(pdftools)
|
||
|
|
library(stringr)
|
||
|
|
library(openxlsx)
|
||
|
|
library(evd)
|
||
|
|
# library(fitdistrplus)
|
||
|
|
|
||
|
|
RestrMF <- function(data, M) {
|
||
|
|
all_l <- melt(data, id.vars="uniDoses", variable.name="replname", value.name="readout")
|
||
|
|
all_l$sample <- c(rep(0,nrow(all_l)/2), rep(1,nrow(all_l)/2))
|
||
|
|
all_l$isRef <- c(rep(1,nrow(all_l)/2), rep(0,nrow(all_l)/2))
|
||
|
|
all_l$log_dose <- log(all_l$uniDoses)
|
||
|
|
CORro <- cor(all_l$uniDoses[1:nrow(all_l)], all_l$readout[1:nrow(all_l)])
|
||
|
|
if (CORro<0) B <- -1 else B <- 1
|
||
|
|
|
||
|
|
startlist <- list(a= min(all_l$readout), b = B, cs = mean(all_l$log_dose),
|
||
|
|
r = 0.0001, d = max(all_l$readout))
|
||
|
|
mr <- tryCatch({
|
||
|
|
gsl_nls(fn=readout ~ a + (d-a)/(1+exp(b*((cs-r*sample)-log_dose))),
|
||
|
|
data = all_l,
|
||
|
|
start= startlist, control = gsl_nls_control(xtol=1e-6, ftol=1e-6, gtol=1e-6))
|
||
|
|
}, error = function(msg) {
|
||
|
|
return(0)
|
||
|
|
})
|
||
|
|
if (length(mr)>1) {
|
||
|
|
s_mr_coef <- summary(mr)$coefficients
|
||
|
|
s_mr <- summary(mr)
|
||
|
|
} else {
|
||
|
|
s_mr_coef <- rep(0,4); s_mr <- 0
|
||
|
|
}
|
||
|
|
|
||
|
|
if (M == "R") {
|
||
|
|
return(s_mr_coef)
|
||
|
|
} else if (M == "CI") {
|
||
|
|
if (length(mr) == 1) return(rep(0,4))
|
||
|
|
RelPot_mr <- exp(s_mr_coef[4,1])
|
||
|
|
POTr_CI <- exp(confint(mr, "r", method="asymptotic"))
|
||
|
|
|
||
|
|
# Pure error
|
||
|
|
FitAnova <- anova(lm(readout ~ factor(uniDoses)*sample, all_l))
|
||
|
|
meanPureErr <- FitAnova[4,3]
|
||
|
|
SEsPure <- sqrt(diag(vcov(mr)/s_mr$sigma^2)*meanPureErr)
|
||
|
|
|
||
|
|
lCIpure <- exp(s_mr_coef[4,1]-qt(0.975,nrow(all_l)-16)*SEsPure[4])
|
||
|
|
uCIpure <- exp(s_mr_coef[4,1]+qt(0.975,nrow(all_l)-16)*SEsPure[4])
|
||
|
|
if (is.infinite(uCIpure)) uCIpure <- NA
|
||
|
|
if (is.infinite(POTr_CI[2])) POTr_CI[2] <- NA
|
||
|
|
relCIpure <- c(lCIpure/RelPot_mr, uCIpure/RelPot_mr)
|
||
|
|
return(c(RelPot_mr, POTr_CI, lCIpure, uCIpure))
|
||
|
|
} else if (M == "U") {
|
||
|
|
if (length(mr) == 1) return(rep(0,4))
|
||
|
|
#browser()
|
||
|
|
startlistmu <- list(as = min(all_l$readout), bs = B, cs = mean(all_l$log_dose), ds = max(all_l$readout),
|
||
|
|
at = min(all_l$readout), bt = B, ct = mean(all_l$log_dose), dt = min(all_l$readout))
|
||
|
|
mu <- tryCatch({
|
||
|
|
gsl_nls(readout ~ as*isRef + at*sample + (ds*isRef + dt*sample - as*isRef - at*sample)/
|
||
|
|
(1 + isRef*exp(bs*(cs-log_dose)) + sample*exp(bt*(ct-log_dose))),
|
||
|
|
data = all_l,
|
||
|
|
start = startlistmu,
|
||
|
|
control = gsl_nls_control(xtol=1e-10, ftol=1e-10, gtol=1e-10))
|
||
|
|
}, error = function(msg) {
|
||
|
|
return(0)
|
||
|
|
})
|
||
|
|
if (length(mu)>1) {
|
||
|
|
smu_coef <- tryCatch({
|
||
|
|
summary(mu)$coefficients
|
||
|
|
}, error = function(msg) {
|
||
|
|
return(rep(NA,8))
|
||
|
|
})
|
||
|
|
return(smu_coef)
|
||
|
|
} else return(rep(NA,8))
|
||
|
|
|
||
|
|
} else return()
|
||
|
|
}
|
||
|
|
|
||
|
|
ui <- fluidPage(
|
||
|
|
useShinyjs(),
|
||
|
|
titlePanel("PDF Scraper"),
|
||
|
|
tabsetPanel(id="toptab",
|
||
|
|
tabPanel("Data loading",
|
||
|
|
wellPanel(
|
||
|
|
fluidRow(
|
||
|
|
# use_busy_spinner(
|
||
|
|
# spin = "cube_grid",
|
||
|
|
# color = "#122440",
|
||
|
|
# position = "top-left",
|
||
|
|
# margins = c(200,330),
|
||
|
|
# height = "50px",
|
||
|
|
# width = "50px"
|
||
|
|
# ),
|
||
|
|
column(2,
|
||
|
|
tags$img(src = "Plateflow.png", class="adv_logo"),
|
||
|
|
h4("Highlight all pdfs (at least 3)"),
|
||
|
|
fileInput(inputId = "iFile", label = "", multiple = T, accept = "application/pdf"),
|
||
|
|
downloadButton('downloadPLA', "Download scraped data"),
|
||
|
|
# h5("Author:")
|
||
|
|
),
|
||
|
|
column(6, style = "background: lightgrey",
|
||
|
|
h4("Sigmoid plots (legend numbers refer to the order of uploaded pdfs - see list below)"),
|
||
|
|
plotOutput("sigPlotREF"),
|
||
|
|
plotOutput("sigPlotTEST"),
|
||
|
|
plotOutput("histCIs"),
|
||
|
|
plotOutput("histCIsPure"),
|
||
|
|
plotOutput("GumbelPlot"),
|
||
|
|
tableOutput("CalcPotDF")
|
||
|
|
),
|
||
|
|
column(4,
|
||
|
|
plotOutput("histEC50REF"),
|
||
|
|
plotOutput("histLasREF"),
|
||
|
|
plotOutput("histUasREF"),
|
||
|
|
tableOutput("ListofPDFsF")
|
||
|
|
)
|
||
|
|
)
|
||
|
|
))
|
||
|
|
|
||
|
|
)
|
||
|
|
|
||
|
|
)
|
||
|
|
|
||
|
|
#### Server ----
|
||
|
|
|
||
|
|
server <- function(input, output, session) {
|
||
|
|
Dat <- reactiveValues()
|
||
|
|
PLOTS <- reactiveValues()
|
||
|
|
|
||
|
|
observe({
|
||
|
|
if (!is.null(input$iFile)) {
|
||
|
|
inFile <- input$iFile
|
||
|
|
filenames <- inFile$name
|
||
|
|
ldf <- lapply(inFile$datapath, pdf_text)
|
||
|
|
Dat$PDFs <- ldf
|
||
|
|
Dat$FNames <- filenames
|
||
|
|
}
|
||
|
|
})
|
||
|
|
|
||
|
|
observeEvent(input$iFile, {
|
||
|
|
show_spinner()
|
||
|
|
})
|
||
|
|
|
||
|
|
observe({
|
||
|
|
if (!is.null(input$iFile)) {
|
||
|
|
|
||
|
|
PDFs <- Dat$PDFs
|
||
|
|
filenames <- Dat$FNames
|
||
|
|
POTlist <- FINALresponses <- SampleNamesL <- list()
|
||
|
|
DilSerVec <- vector()
|
||
|
|
hide_spinner()
|
||
|
|
for (Nfile in 1:length(PDFs)) {
|
||
|
|
tt = PDFs[[Nfile]]
|
||
|
|
PageI <- strg <- POT <- vector(); resIND <- matrix(NA, ncol=2,nrow=3)
|
||
|
|
T1flag <- T2flag <- StFlag <- 0
|
||
|
|
|
||
|
|
for (Seite in 1:length(tt)) {
|
||
|
|
Zeilen <- strsplit(tt[Seite], "\n")
|
||
|
|
REGEXloc <- grep(pattern='Dose .alue', Zeilen[[1]])
|
||
|
|
if (length(REGEXloc)>0) {
|
||
|
|
#### get Standard ----
|
||
|
|
for (n in 1:length(REGEXloc)) {
|
||
|
|
print(paste("Response page no.:", Seite, "location", REGEXloc[n]))
|
||
|
|
PageI <- c(PageI, Seite)
|
||
|
|
strg <- c(strg, REGEXloc[n])
|
||
|
|
if (StFlag == 0) {
|
||
|
|
grepStS <- grep("Standard .ample", Zeilen[[1]])
|
||
|
|
if (length(grepStS)>0) {
|
||
|
|
for (z in 1:length(grepStS)) {
|
||
|
|
if (abs(REGEXloc[n]-grepStS[z]) <5) {
|
||
|
|
resIND[1,] <- c(Seite, REGEXloc[n])
|
||
|
|
REF <- gsub("Standard .ample: ","",Zeilen[[1]][grepStS[z]])
|
||
|
|
StFlag <- 1
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
#### get Test ----
|
||
|
|
if (T1flag == 0) {
|
||
|
|
grepT3 <- grep("Test .ample", Zeilen[[1]])
|
||
|
|
if (length(grepT3)>0) {
|
||
|
|
for (z in 1:length(grepT3)) {
|
||
|
|
if (abs(REGEXloc[n]-grepT3[z]) <5) {
|
||
|
|
resIND[2,] <- c(Seite, REGEXloc[n])
|
||
|
|
TEST1 <- gsub("Test .ample: ","",Zeilen[[1]][grepT3[z]])
|
||
|
|
T1flag <- 1
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|
||
|
|
} else TESTflag <- 1
|
||
|
|
}
|
||
|
|
if (T1flag == 1) {
|
||
|
|
grepT4 <- grep("Test .ample", Zeilen[[1]])
|
||
|
|
if (length(grepT4)>0) {
|
||
|
|
for (z in 1:length(grepT4)) {
|
||
|
|
if (abs(REGEXloc[n]-grepT4[z]) <5) {
|
||
|
|
resIND[3,] <- c(Seite, REGEXloc[n])
|
||
|
|
TEST2 <- gsub("Test .ample: ","",Zeilen[[1]][grepT4[z]])
|
||
|
|
T2flag <- 1
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|
||
|
|
} else TESTflag <- 1
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
#### Potency from PDF ----
|
||
|
|
POTloc <- grep(pattern='Potency .atio', Zeilen[[1]])
|
||
|
|
if (length(POTloc)>0) {
|
||
|
|
for (n in 1:length(POTloc)) {
|
||
|
|
POT <- c(POT, Zeilen[[1]][POTloc:(POTloc+5)])
|
||
|
|
}
|
||
|
|
}
|
||
|
|
} # tt
|
||
|
|
if (sum(resIND[2,] == resIND[3,]) ==2) { resIND[3,] <- c(NA,NA) }
|
||
|
|
|
||
|
|
POTlist[[Nfile]] <- POT
|
||
|
|
#### geet responses ----
|
||
|
|
rm(ALLE3)
|
||
|
|
if (all(is.na(resIND[3,]))) ProdsinPDF <- 1:2 else if (all(is.na(resIND[2,]))) ProdsinPDF <- c(1,3) else ProdsinPDF <- 1:3
|
||
|
|
if (all(is.na(resIND[2:3,]))) next
|
||
|
|
for (x in ProdsinPDF) {
|
||
|
|
ZeilenR <- strsplit(tt[resIND[x,1]], "\n")[[1]]
|
||
|
|
ZeilenREF <- ZeilenR[resIND[x,2]:length(ZeilenR)]
|
||
|
|
grepDoses <- grep("Dose .alue", ZeilenREF)
|
||
|
|
Doses <- unlist(regmatches(c(ZeilenREF[grepDoses[1]], ZeilenREF[grepDoses[2]]),
|
||
|
|
gregexpr("([0-9]+)\\.?([0-9]+)",
|
||
|
|
c(ZeilenREF[grepDoses[1]], ZeilenREF[grepDoses[2]]))))
|
||
|
|
uniDoses <- as.numeric(unique(Doses))
|
||
|
|
Ndoses <- length(uniDoses)
|
||
|
|
grepResponses <- grep(".esponse", ZeilenREF)
|
||
|
|
grepMean <- grep(".ean", ZeilenREF)
|
||
|
|
NoResp <- grepMean[1]-grepResponses[1]
|
||
|
|
|
||
|
|
IND <- c(grepDoses)
|
||
|
|
StepIX <- IND+1
|
||
|
|
INDresp1 <- grepResponses
|
||
|
|
INDresp2 <- grepMean-1
|
||
|
|
Responses <- list()
|
||
|
|
for (n in 1:length(IND)) {
|
||
|
|
Matches <- unlist(regmatches(ZeilenREF[INDresp1[n]:INDresp2[n]],
|
||
|
|
gregexpr("([0-9]+)\\.?([0-9]+)",
|
||
|
|
ZeilenREF[INDresp1[n]:INDresp2[n]])))
|
||
|
|
Responses[[n]] <- as.numeric(Matches)
|
||
|
|
}
|
||
|
|
Step <- unlist(regmatches(ZeilenREF[StepIX[1]], gregexpr("([0-9]+)", ZeilenREF[StepIX[1]])))
|
||
|
|
maxStep <- max(as.numeric(Step))
|
||
|
|
|
||
|
|
resStep <- Ndoses-maxStep
|
||
|
|
if (maxStep== (Ndoses-1)) {
|
||
|
|
ref_data <- data.frame(c(Responses[[1]][1:maxStep], Responses[[2]][1]),
|
||
|
|
c(Responses[[1]][(maxStep+1):(maxStep*2)], Responses[[2]][2]),
|
||
|
|
c(Responses[[1]][(maxStep*2+1):(maxStep*3)], Responses[[2]][3]))
|
||
|
|
} else if (maxStep< (Ndoses-1)) {
|
||
|
|
ref_data <- data.frame(c(Responses[[1]][1:maxStep], Responses[[2]][1:resStep]),
|
||
|
|
c(Responses[[1]][(maxStep+1):(maxStep*2)], Responses[[2]][(resStep+1):(resStep*2)]),
|
||
|
|
c(Responses[[1]][(maxStep*2+1):(maxStep*3)], Responses[[2]][(resStep*2+1):(resStep*3)]))
|
||
|
|
} else {
|
||
|
|
ref_data <- data.frame(c(Responses[[1]][1:maxStep]),
|
||
|
|
c(Responses[[1]][(maxStep+1):(maxStep*2)]),
|
||
|
|
c(Responses[[1]][(maxStep*2+1):(maxStep*3)]))
|
||
|
|
}
|
||
|
|
|
||
|
|
if (x==1) colnames(ref_data) <- c(paste0(REF, "_1"), paste0(REF, "_2"), paste0(REF, "_3"))
|
||
|
|
if (x==2) colnames(ref_data) <- c(paste0(TEST1, "_1"), paste0(TEST1, "_2"), paste0(TEST1, "_3"))
|
||
|
|
if (x==3) colnames(ref_data) <- c(paste0(TEST2, "_1"), paste0(TEST2, "_2"), paste0(TEST2, "_3"))
|
||
|
|
|
||
|
|
if (!exists("ALLE3")) {
|
||
|
|
ALLE3 <- ref_data
|
||
|
|
} else { ALLE3 <- cbind(ALLE3, ref_data) }
|
||
|
|
|
||
|
|
} # loop ProdsinPDF
|
||
|
|
ALLE3_ <- Filter(function(x) !all(is.na(x)), ALLE3)
|
||
|
|
ALLE3 <- cbind(uniDoses, ALLE3_)
|
||
|
|
FINALresponses[[Nfile]] <- ALLE3
|
||
|
|
SampleNamesL[[Nfile]] <- c(REF, TEST1, TEST2)
|
||
|
|
DilSerVec <- c(DilSerVec, NoResp)
|
||
|
|
|
||
|
|
} # loop Nfile
|
||
|
|
|
||
|
|
Dat$FINALreponses <- FINALresponses
|
||
|
|
Dat$POTlist <- POTlist
|
||
|
|
Dat$DilSerVec <- DilSerVec
|
||
|
|
Dat$SampleNamesL <- SampleNamesL
|
||
|
|
} # if (iFile)
|
||
|
|
})
|
||
|
|
|
||
|
|
observe({
|
||
|
|
if (!is.null(Dat$FINALresponses)) {
|
||
|
|
filenames <- Dat$FNames
|
||
|
|
FINALresponses <- Dat$FINALresponses
|
||
|
|
POTlist <- Dat$POTlist
|
||
|
|
DilSerVec <- Dat$DilSerVec
|
||
|
|
rm(SIGrefDF, SIGtestDF)
|
||
|
|
CalcPot <- RestrM <- UnrestrM <- list()
|
||
|
|
for (pdfInd in 1:length(FINALresponses)) {
|
||
|
|
Potratio <- POTlist[[pdfInd]]
|
||
|
|
getPotratio <- unlist(regmatches(Potratio[1],
|
||
|
|
gregexpr("([0-9]+)\\.?([0-9]+)",
|
||
|
|
Potratio[1])))
|
||
|
|
Alle3 <- FINALresponses[[pdfInd]]
|
||
|
|
if (is.null(Alle3)) next
|
||
|
|
if (DilSerVec[pdfInd] == 3) {
|
||
|
|
StS <- Alle3[,1:4]
|
||
|
|
TestSs <- Alle3[,c(5:length(Alle3))]
|
||
|
|
StTest1 <- cbind(StS, TestSs[,1:3])
|
||
|
|
if (ncol(TestSs) >3) StTest2 <- cbind(StS, TestSs[,4:6])
|
||
|
|
|
||
|
|
} else if (DilSerVec[pdfInd] == 2) {
|
||
|
|
StS <- Alle3[,1:3]
|
||
|
|
TestSs <- Alle3[,c(4:length(Alle3))]
|
||
|
|
StTest1 <- cbind(StS, TestSs[,1:2])
|
||
|
|
if (ncol(TestSs) >2) StTest2 <- cbind(StS, TestSs[,3:4])
|
||
|
|
}
|
||
|
|
PotM1_1 <- RestrMF(StTest1, M="CI")
|
||
|
|
if (ncol(TestSs)/DilSerVec[pdfInd] ==2) {
|
||
|
|
PotM1_2 <- RestrMF(StTest2, M="CI")
|
||
|
|
PotM1 <- data.frame(rbind(unlist(PotM1_1), unlist(PotM1_2)))
|
||
|
|
} else { PotM1 <- data.frame(t(PotM1_1)) }
|
||
|
|
colnames(PotM1) <- c("rel. potency", "lowerCI", "upperCI","lowerCIpureEr", "upperCIpureEr")
|
||
|
|
|
||
|
|
PotM1_ <- as.matrix(PotM1)
|
||
|
|
colnames(PotM1_) <- names(PotM1)
|
||
|
|
PotM1 <- cbind(rep(filenames[pdfInd], nrow(PotM1_)), PotM1_)
|
||
|
|
CalcPot[[pdfInd]] <- PotM1_
|
||
|
|
if (!exists("CalcPotDF")) CalcPotDF <- PotM1_ else CalcPotDF <- rbind(CalcPotDF, PotM1_)
|
||
|
|
|
||
|
|
RMcoefs1 <- RestrMF(StTest1, M="R")
|
||
|
|
if (ncol(TestSs)/DilSerVec[pdfInd] ==2) {
|
||
|
|
RMcoefs2 <- RestrMF(StTest2, M="R")
|
||
|
|
RMcoefs <- rbind(c(basename(filenames[pdfInd]), NA, NA, NA), RMcoefs1, rep(NA,4), RMcoefs2)
|
||
|
|
|
||
|
|
} else { RMcoefs <- rbind(c(basename(filenames[pdfInd]), NA, NA, NA), RMcoefs1) }
|
||
|
|
RestrM[[pdfInd]] <- RMcoefs
|
||
|
|
if (!exists("RMcoefsDF")) RMcoefsDF <- RMcoefs[,1] else RMcoefsDF <- rbind(RMcoefsDF, RMcoefs[,1])
|
||
|
|
|
||
|
|
URMcoefs1 <- RestrMF(StTest1, M="U")
|
||
|
|
if (ncol(TestSs)/DilSerVec[pdfInd] ==2) {
|
||
|
|
URMcoefs2 <- RestrMF(StTest2, M="U")
|
||
|
|
URMcoefs <- rbind(c(basename(filenames[pdfInd]), NA, NA, NA), URMcoefs1, rep(NA,4), URMcoefs2)
|
||
|
|
|
||
|
|
} else { URMcoefs <- rbind(c(basename(filenames[pdfInd]), NA, NA, NA), URMcoefs1) }
|
||
|
|
UnrestrM[[pdfInd]] <- URMcoefs
|
||
|
|
if (!exists("URMcoefsDF")) URMcoefsDF <- URMcoefs[,1] else URMcoefsDF <- rbind(URMcoefsDF, URMcoefs[,1])
|
||
|
|
|
||
|
|
X <- seq(min(log(Alle3$uniDoses)), max(log(Alle3$uniDoses)), 0.1)
|
||
|
|
sigRef <- URMcoefs1[1,1] + (URMcoefs1[4,1]-URMcoefs1[1,1])/(1+exp(URMcoefs1[2,1]*(URMcoefs1[3,1]-X)))
|
||
|
|
sigTest1 <- URMcoefs1[5,1] + (URMcoefs1[8,1]-URMcoefs1[5,1])/(1+exp(URMcoefs1[6,1]*(URMcoefs1[7,1]-X)))
|
||
|
|
if (exists("URMcoefs2")) {
|
||
|
|
if (!all(is.na(URMcoefs2)) & sum(URMcoefs2) != 2) {
|
||
|
|
sigTest1 <- URMcoefs2[5,1] + (URMcoefs2[8,1]-URMcoefs2[5,1])/(1+exp(URMcoefs2[6,1]*(URMcoefs2[7,1]-X)))
|
||
|
|
}
|
||
|
|
}
|
||
|
|
dfPlotsigRef <- data.frame(X=X, sigRef = sigRef, Prod = pdfInd)
|
||
|
|
dfPlotsigTest1 <- data.frame(X=X, sigTest = sigTest1, Prod = paste0(pdfInd, "_1"))
|
||
|
|
if (exists("URMcoefs2")) {
|
||
|
|
if (!all(is.na(URMcoefs2))) {
|
||
|
|
dfPlotsigTest2 <- data.frame(X=X, sigTest = sigTest2, Prod = paste0(pdfInd, "_2"))
|
||
|
|
}
|
||
|
|
}
|
||
|
|
if (!exists("SIGrefDF")) SIGrefDF <- dfPlotsigRef else SIGrefDF <- rbind(SIGrefDF, dfPlotsigRef)
|
||
|
|
if (!exists("SIGtestDF")) {
|
||
|
|
if (exists("dfPlotsigTest2")) SIGtestDF <- rbind(dfPlotsigTest1, dfPlotsigTest2) else SIGtestDF <- dfPlotsigTest1
|
||
|
|
} else {
|
||
|
|
if (exists("dfPlotsigTest2")) SIGtestDF <- rbind(SIGtestDF,dfPlotsigTest1, dfPlotsigTest2) else SIGtestDF <- rbind(dfPlotsigTest1, dfPlotsigTest2)
|
||
|
|
}
|
||
|
|
} # pdfInd
|
||
|
|
|
||
|
|
|
||
|
|
if (ncol(URMcoefsDF)>11) EC50TEST <- as.numeric(c(URMcoefsDF[,8], URMcoefsDF[,17])) else EC50TEST <- as.numeric(c(URMcoefsDF[,8]))
|
||
|
|
EC50TEST <- EC50TEST[!EC50TEST %in% boxplot.stats(EC50TEST)$out]
|
||
|
|
EC50REF <- as.numeric(URMcoefsDF[,4])
|
||
|
|
EC50REF <- EC50REF[!EC50REF %in% boxplot.stats(EC50REF)$out]
|
||
|
|
UasREF <- as.numeric(URMcoefsDF[,5])
|
||
|
|
UasREF <- UasREF[!UasREF %in% boxplot.stats(UasREF)$out]
|
||
|
|
LasREF <- as.numeric(URMcoefsDF[,2])
|
||
|
|
LasREF <- LasREF[!LasREF %in% boxplot.stats(LasREF)$out]
|
||
|
|
|
||
|
|
Dat$URMcoefsDF <- URMcoefsDF
|
||
|
|
Dat$RestrM <- RestrM
|
||
|
|
Dat$CalcPot <- CalcPot
|
||
|
|
|
||
|
|
#### sigmoid plots ----
|
||
|
|
Slope <- as.numeric(URMcoefsDF[1,3])
|
||
|
|
if (Slope > 0) {
|
||
|
|
x_UA <- max(X); x_LA <- min(X)
|
||
|
|
} else { x_UA <- min(X); x_LA <- max(X) }
|
||
|
|
|
||
|
|
p1 <- ggplot(SIGrefDF, aes(x_X, y=sigRef, col=as.factor(Prod))) +
|
||
|
|
geom_line() +
|
||
|
|
annotate("text", label="x", x=x_UA, y=UasREF, alpha=0.2) +
|
||
|
|
annotate("text", label="o", x=x_LA, y=LasREF, alpha=0.2) +
|
||
|
|
geom_vline(xintercept = EC50REF, alpha = 0.2) +
|
||
|
|
xlab("dilutions") +
|
||
|
|
ggtitle("Plot of all calculated reference fits (unrestricted model, in gray vertical lines: EC50)") +
|
||
|
|
theme_bw() +
|
||
|
|
theme(axis.text = element_text(face = "bold", size = 15),
|
||
|
|
plot.title = element_text(size = 15, face = "bold"))
|
||
|
|
|
||
|
|
output$sigPlotREF <- renderPlot({ p1 })
|
||
|
|
|
||
|
|
PLOTS$sigPlotREF <- p1
|
||
|
|
|
||
|
|
p2 <- ggplot(SIGtestDF, aes(x_X, y=sigTest, col=as.factor(Prod))) +
|
||
|
|
geom_line() +
|
||
|
|
#annotate("text", label="x", x=x_UA, y=UasREF, alpha=0.2) +
|
||
|
|
#annotate("text", label="o", x=x_LA, y=LasREF, alpha=0.2) +
|
||
|
|
geom_vline(xintercept = EC50TEST, alpha = 0.2) +
|
||
|
|
xlab("dilutions") +
|
||
|
|
ggtitle("Plot of all calculated reference fits (unrestricted model, in gray vertical lines: EC50)") +
|
||
|
|
theme_bw() +
|
||
|
|
theme(axis.text = element_text(face = "bold", size = 15),
|
||
|
|
plot.title = element_text(size = 15, face = "bold"))
|
||
|
|
|
||
|
|
output$sigPlotREF <- renderPlot({ p2 })
|
||
|
|
|
||
|
|
PLOTS$sigPlotTEST <- p2
|
||
|
|
|
||
|
|
|
||
|
|
#### histograms ----
|
||
|
|
output$histEC50REF <- renderPlot({
|
||
|
|
hist(EC50REF, main = 'Histogram of EC50REF')
|
||
|
|
})
|
||
|
|
output$histLasREF <- renderPlot({
|
||
|
|
hist(Las0REF, main = 'Histogram of lower asymptotes REF')
|
||
|
|
})
|
||
|
|
output$histUasREF <- renderPlot({
|
||
|
|
hist(UasREF, main = 'Histogram of upper asymptotes REF')
|
||
|
|
})
|
||
|
|
PLOTS$histEO50REF <- hist(EC50REF, main = 'Histogram of EC50REF')
|
||
|
|
PLOTS$histLasREF <- hist(LasREF, main = 'Histogram of EC50REF')
|
||
|
|
PLOTS$histUasREF <- hist(UasREF, main = 'Histogram of EC50REF')
|
||
|
|
|
||
|
|
#### Calculated Potencies table ----
|
||
|
|
|
||
|
|
colnames(CalcPotDF) <- c("pdf","rel. potency","lowerCI","upperCI","lower CI puerErr","upper CI pureErr")
|
||
|
|
SampleNamesL <- Dat$SampleNamesL
|
||
|
|
SampleNames <- unlist(SampleNamesL)
|
||
|
|
if (length(SampleNames)/length(SampleNamesL) == 3) {
|
||
|
|
REFIndices <- seq(1,length(SampleNamesL))*3-2
|
||
|
|
} else { REFIndices <- seq(1,length(SampleNamesL))*2-1 }
|
||
|
|
Test_Sample_Names <- SampleNames[-c(REFIndices)]
|
||
|
|
|
||
|
|
CalcPotDF <- as.data.frame(CalcPotDF)
|
||
|
|
CalcPotDF[,2:6] <- apply(CalcPotDF[,2:6],2,as.numeric)
|
||
|
|
CalcPotDF$relLCI <- CalcPotDF$lowerCI/CalcPotDF$`rel. potency`
|
||
|
|
CalcPotDF$relUCI <- CalcPotDF$upperCI/CalcPotDF$`rel. potency`
|
||
|
|
CalcPotDF$`relLCI pureErr` <- CalcPotDF$`lowerCI pureErr`/CalcPotDF$`rel. potency`
|
||
|
|
CalcPotDF$`relUCI pureErr` <- CalcPotDF$`upperCI pureErr`/CalcPotDF$`rel. potency`
|
||
|
|
|
||
|
|
CalcPotDF2 <- cbind(CalcPotDF, Test_Sample_Names)
|
||
|
|
Dat$CalcPotDF2 <- CalcPotDF2
|
||
|
|
|
||
|
|
output$CalcPotDF <- renderTable({ CalcPotDF2 })
|
||
|
|
#### CI plots ----
|
||
|
|
CalcPotDF_ <- CalcPotDF[,c(1,7,8)]
|
||
|
|
all_lPot <- melt(as.data.frame(CalcPotDF_, id.vars="pdf",variable.name="var", value.name="Climit"))
|
||
|
|
all_lPot[,3] <- as.numeric(all_lPot[,3])
|
||
|
|
all_lPot[,3][all_lPot[,3] > 5] <- NA
|
||
|
|
all_lPot[,3][all_lPot[,3] < 0.1] <- NA
|
||
|
|
|
||
|
|
P_histCI <- ggplot(all_lPot, aes(x=Climit, fill=var)) +
|
||
|
|
geom_histogram(color="#e9ecef", alpha=0.6, position = "identity") +
|
||
|
|
scale-fill-manual(values=c("darkgreen","darkblue","salmon2","tomato3")) +
|
||
|
|
ggtitle("Histogram of relative potencies, standard RMSEs") +
|
||
|
|
scale_x_continuous(
|
||
|
|
breaks=seq(trunc(min(all_lPot$Climit, na.rm=T)*10)/10, max(all_lPot$Climit, na.rm=T)*1.1, by=0.2),
|
||
|
|
) +
|
||
|
|
theme_bw() +
|
||
|
|
theme(axis.text = element_text(face="bold", size=15),
|
||
|
|
axis.text.x = element_text(angle=90),
|
||
|
|
plot.title= element_text(size=15, face="bold"))
|
||
|
|
|
||
|
|
output$histCIsPure <- renderPlot({ P_histCI })
|
||
|
|
|
||
|
|
|
||
|
|
CalcPotDF_Pure <- CalcPotDF[,c(1,9,10)]
|
||
|
|
all_lPotPure <- melt(as.data.frame(CalcPotDF_Pure, id.vars="pdf",variable.name="var", value.name="Climit"))
|
||
|
|
all_lPotPure[,3][all_lPotPure[,3] == 0] <- NA
|
||
|
|
all_lPotPure[,3][all_lPotPure[,3] > 5] <- NA
|
||
|
|
all_lPotPure[,3][all_lPotPure[,3] < 0.1] <- NA
|
||
|
|
|
||
|
|
P_histCIPure <- ggplot(all_lPotPure, aes(x=Climit, fill=var)) +
|
||
|
|
geom_histogram(color="#e9ecef", alpha=0.6, position = "identity") +
|
||
|
|
scale-fill-manual(values=c("darkgreen","darkblue","salmon2","tomato3")) +
|
||
|
|
ggtitle("Histogram of relative potencies, pure error") +
|
||
|
|
scale_x_continuous(
|
||
|
|
breaks=seq(trunc(min(all_lPotPure$Climit, na.rm=T)*10)/10, max(all_lPotPure$Climit, na.rm=T)*1.1, by=0.2),
|
||
|
|
) +
|
||
|
|
theme_bw() +
|
||
|
|
theme(axis.text = element_text(face="bold", size=15),
|
||
|
|
axis.text.x = element_text(angle=90),
|
||
|
|
plot.title= element_text(size=15, face="bold"))
|
||
|
|
|
||
|
|
output$histCIsPure <- renderPlot({ P_histCIPure })
|
||
|
|
|
||
|
|
ListofPDFs <- sapply(RestrM, function(x) rbind(x[1]))
|
||
|
|
output$ListofPDFs <- renderTable({ ListofPDFs}, rownames=T)
|
||
|
|
|
||
|
|
logCPDF <- log(CalcPotDF[,9:10])
|
||
|
|
|
||
|
|
logCPDF1 <- cbind(CalcPotDF[,1], logCPDF)
|
||
|
|
logCPDF1 <- logCPDF1[!duplicated(logCPDF1[,2:3]),]
|
||
|
|
logCPDF_ <- logCPDF1[!is.na(logCPDF1[,3]),]
|
||
|
|
colnames(logCPDF_) <- c("pdf", "relLCI","relUCI")
|
||
|
|
|
||
|
|
dg <- function(x,loc,scale,log) {
|
||
|
|
r <- try(dgumbel(x,loc,scale,log), silent=T)
|
||
|
|
if (inherits(r, "try-error")) return(NA)
|
||
|
|
return(r)
|
||
|
|
}
|
||
|
|
uCIGumbel <- fitdistr(logCPDF_[,3], dg,start=list(loc=1,scale=1))
|
||
|
|
lCIGumbel <- fitdistr(logCPDF_[,2], dg,start=list(loc=1,scale=1))
|
||
|
|
Gumbel <- c(rev(dgumbel(seq(0,0.5,0.01), loc=uCIGumbel$extimate[1], scale=uCIGumbel$extimate[2])), dgumbel(seq(0,0.5,0.01), loc=uCIGumbel$extimate[1], scale=uCIGumbel$extimate[2]))
|
||
|
|
|
||
|
|
GumbelDF <- as.data.frame(cbind(X=seq(-0.5,0.5,0.01), Gumbel))
|
||
|
|
all_lPotPure <- melt(as.data.frame(logCPDF_), id.vars="pdf",variable.name = "var",value.name="Climit")
|
||
|
|
all_lPotPure[,3][all_lPotPure[,3] == 0] <- NA
|
||
|
|
|
||
|
|
uEAC099 <- exp(qgumbel(0.99, uCIGumbel$estimate[1],uCIGumbel$estimate[2]))*100
|
||
|
|
lEAC001 <- exp(-qgumbel(0.99, uCIGumbel$estimate[1],uCIGumbel$estimate[2]))*100
|
||
|
|
uEAC095 <- exp(qgumbel(0.95, uCIGumbel$estimate[1],uCIGumbel$estimate[2]))*100
|
||
|
|
lEAC005 <- exp(-qgumbel(0.95, uCIGumbel$estimate[1],uCIGumbel$estimate[2]))*100
|
||
|
|
|
||
|
|
output$GumbelPlot <- renderPlot({
|
||
|
|
hist(all_lPotPure$Climit, breaks = 50, xlab="log(relative CLs)",
|
||
|
|
main=paste("calculated EACs 99%:",round(lEAC001,0)), "-", round(uEAC099,0), " 95%", round(lEAC005,0), "-",round(uEAC095,0))
|
||
|
|
lines(GumbelDF$X, GumbelDF$Gumbel)
|
||
|
|
|
||
|
|
|
||
|
|
})
|
||
|
|
}
|
||
|
|
})
|
||
|
|
|
||
|
|
output$downloadPLA <- downloadHandler(
|
||
|
|
filename="PLAcontent.zip",
|
||
|
|
content=function(fname) {
|
||
|
|
fs <- c()
|
||
|
|
tmpdir <- tempdir()
|
||
|
|
fileOutUNRM=paste(paste0(tmpdir,sep='/', "Coefficients_UnrestrModel"), sep='','.xlsx')
|
||
|
|
fs=c(fs, fileOutUNRM)
|
||
|
|
URMcoelsDF <- Dat$URMcoefsDF
|
||
|
|
write.xlsx(URMcoefsDF, fileOutUNRM, rowNames=T)
|
||
|
|
|
||
|
|
fileOutPOT=paste(paste0(tmpdir,sep='/', "relPot_CIs"), sep='','.xlsx')
|
||
|
|
fs=c(fs, fileOutPOT)
|
||
|
|
CalcPotDF <- Dat$CalcPotDF
|
||
|
|
write.xlsx(CalcPotDF, fileOutPOT, rowNames=T)
|
||
|
|
|
||
|
|
sigPlotREF <- PLOTS$sigPlotREF
|
||
|
|
sigPlotTEST <- PLOTS$sigPlotTEST
|
||
|
|
fileOutSigREF=paste(paste0(tmpdir,sep='/', "_SigmoidsREF"), sep='','.png')
|
||
|
|
fs=c(fs, fileOutSigREF)
|
||
|
|
png(fileOutSigREF, width=600, height=400)
|
||
|
|
plot(sigPlotREF)
|
||
|
|
dev.off()
|
||
|
|
|
||
|
|
fileOutSigTEST=paste(paste0(tmpdir,sep='/', "_SigmoidsTEST"), sep='','.png')
|
||
|
|
fs=c(fs, fileOutSigTEST)
|
||
|
|
png(fileOutSigTEST, width=600, height=400)
|
||
|
|
plot(sigPlotTEST)
|
||
|
|
dev.off()
|
||
|
|
|
||
|
|
fileOutRM=paste(paste0(tmpdir,sep='/', "_RestrictedModel"), sep='','.xlsx')
|
||
|
|
fileOutCalcPot=paste(paste0(tmpdir,sep='/', "_CalculatedPotencies"), sep='','.xlsx')
|
||
|
|
fileOutResponses=paste(paste0(tmpdir,sep='/', "_Responses"), sep='','.xlsx')
|
||
|
|
|
||
|
|
fs=c(fs, fileOutRM,fileOutCalcPot,fileOutResponses)
|
||
|
|
RestrM <- Dat$RestrM
|
||
|
|
CalcPot <- Dat$CalcPot
|
||
|
|
FINALresponses <- Dat$FINALresponses
|
||
|
|
write.xlsx(RestrM, fileOutRM, rowNames=T)
|
||
|
|
write.xlsx(CalcPot, fileOutCalcPot, rowNames=F)
|
||
|
|
write.xlsx(FINALresponses, fileOutResponses, rowNames=F)
|
||
|
|
|
||
|
|
zip::zipr(zipfile=fname, fileas=fs, include_directories = F)
|
||
|
|
|
||
|
|
}, contentType = "application/zip"
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
shinyApp(ui=ui, server=server)
|