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if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc"))
checkexperiment <- function(id, db = "ecotox", endpoint = "%")
{
databases <- data.frame(
responsename=c("viability","activity","response"),
testtype=c("celltype","enzyme","organism"),
exptype=c("plate","plate","experiment"))
rownames(databases) <- c("cytotox","enzymes","ecotox")
if (!(db %in% rownames(databases))) stop("Database is not supported")
if (requireNamespace("RODBC")) {
channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower")
} else {
stop("For this function, the RODBC package has to be installed and configured.")
}
responsename = as.character(databases[db,1])
testtype = as.character(databases[db,2])
exptype = as.character(databases[db,3])
exptable <- paste(exptype, "s", sep="")
commentquery <- paste("SELECT comment FROM ", exptable ,
" WHERE ", exptype, " = ", id)
commentdata <- RODBC::sqlQuery(channel,commentquery)
comment <- as.character(commentdata[[1]])
expquery <- paste("SELECT experimentator,substance, ",
testtype, ",conc,unit,", responsename, ",performed,ok",
" FROM ",db," WHERE ",exptype,"=", id,
sep = "")
if (db == "ecotox") {
expquery <- paste(expquery, " AND type LIKE '",
endpoint, "'", sep = "")
}
expdata <- RODBC::sqlQuery(channel,expquery)
if (db %in% c("cytotox","enzymes")) {
controlquery <- paste("SELECT type,response FROM controls
WHERE plate=",id)
controldata <- RODBC::sqlQuery(channel,controlquery)
}
RODBC::odbcClose(channel)
op <- par(ask=TRUE)
on.exit(par(op))
if (db %in% c("cytotox","enzymes")) {
blinds <- subset(controldata,type=="blind")
controls <- subset(controldata,type=="control")
numberOfBlinds <- length(blinds$response)
meanOfBlinds <- signif(mean(blinds$response),2)
stdOfBlinds <- signif(sd(blinds$response),2)
} else {
controls <- subset(expdata,conc == 0)
expdata <- subset(expdata, conc != 0)
numberOfBlinds <- NA
meanOfBlinds <- NA
stdOfBlinds <- NA
}
numberOfControls <- length(controls$response)
if (numberOfControls > 0) {
meanOfControls <- signif(mean(controls$response),2)
stdOfControls <- signif(sd(controls$response),2)
percentstdOfcontrols <-signif(stdOfControls *100/meanOfControls,2)
} else {
meanOfControls <- stdOfControls <- percentstdOfcontrols <- NA
}
if (length(expdata$experimentator) < 1) {
stop("There is no response data for ",exptype," ",
id," in database ",db,"\n")
}
exptypestring <- paste(toupper(substring(exptype,1,1)),
substring(exptype,2),sep="")
expdata$experimentator <- factor(expdata$experimentator)
expdata$type <- factor(expdata[[testtype]])
expdata$performed <- factor(as.character(expdata$performed))
expdata$substance <- factor(expdata$substance)
expdata$unit <- factor(expdata$unit)
expdata$ok <- factor(expdata$ok)
cat("\n",exptypestring,id,"from database",db,":\n\n",
"\tExperimentator(s):\t",levels(expdata$experimentator),"\n",
"\tType(s):\t\t",levels(expdata$type),"\n",
"\tPerformed on:\t\t",levels(expdata$performed),"\n",
"\tSubstance(s):\t\t",levels(expdata$substance),"\n",
"\tConcentration unit(s):\t",levels(expdata$unit),"\n",
"\tComment:\t\t",comment,"\n",
"\tOK Levels:\t\t\t",levels(expdata$ok),"\n",
"\t\tNumber \tMean \tStd. Dev. \t% Std. Dev.\n",
"\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",
"\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",
stdOfControls,"\t\t",percentstdOfcontrols,"\n")
if (db == "ecotox") {
boxplot(controls$response,
names="controls",
ylab="Response",
ylim=c(0,max(controls$response)),
boxwex=0.4,
main=paste("Plate ",id))
} else {
boxplot(blinds$response,controls$response,
names=c("blinds","controls"),
ylab="Response",
boxwex=0.4,
main=paste("Plate ",id))
}
drdata <- expdata[c(2,4,6)]
drdata$substance <- factor(drdata$substance)
substances <- levels(drdata$substance)
lld <- log10(min(subset(drdata,conc!=0)$conc))
lhd <- log10(max(drdata$conc))
plot(1,type="n",
xlim=c(lld - 0.5, lhd + 2),
ylim= c(-0.1, 2),
xlab=paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
ylab=responsename)
drdatalist <- split(drdata,drdata$substance)
for (i in 1:length(drdatalist)) {
points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsename]],col=i);
}
legend("topright",substances, pch=1, col=1:length(substances), inset=0.05)
title(main=paste(levels(expdata$experimentator),
" - ",levels(expdata$type)))
}
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