utils::globalVariables(c("type", "conc", "substance"))
checkexperiment <- function(id,
db = c("ecotox", "cytotox", "enzymes"),
endpoint = "%", whereClause = "1")
{
db = match.arg(db)
databases <- data.frame(
responsename = c("viability", "activity", "raw_response"),
testtype = c("celltype", "enzyme", "organism"),
exptype = c("plate", "plate", "experiment"),
row.names = c("cytotox", "enzymes", "ecotox"),
stringsAsFactors = FALSE)
con <- dbConnect(odbc(), "cytotox", database = db)
responsename <- databases[db, 1]
testtype <- databases[db, 2]
exptype <- databases[db, 3]
exptable <- paste(exptype, "s", sep = "")
commentquery <- paste0("SELECT comment FROM ", exptable, " ",
"WHERE ", exptype, " = ", id)
commentdata <- dbGetQuery(con, commentquery)
comment <- as.character(commentdata[[1]])
expquery <- paste0("SELECT ",
"experimentator, substance, ", testtype, ", conc, unit, ", responsename, ", ",
if (db == "ecotox") "type, raw_0, duration, ",
"performed, ok ",
"FROM ", db, " ",
"WHERE ", exptype, "=", id)
if (db == "ecotox") {
expquery <- paste0(expquery, " AND type LIKE '", endpoint, "' AND ", whereClause)
}
expdata <- dbGetQuery(con, expquery)
if (db %in% c("cytotox", "enzymes")) {
controlquery <- paste0("SELECT type, response FROM controls ",
" WHERE plate=", id)
controldata <- dbGetQuery(con, controlquery)
}
op <- par(ask=TRUE)
on.exit(par(op))
if (db %in% c("cytotox","enzymes")) {
blinds <- subset(controldata, type == "blind")
controls <- subset(controldata, type == "control")
QA <- matrix(nrow = 2, ncol = 4,
dimnames = list(c("Blind", "Control (conc = 0)"),
c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
QA[1, 1] <- length(blinds$response)
QA[1, 2] <- signif(mean(blinds$response), 2)
QA[1, 3] <- signif(sd(blinds$response), 2)
QA[1, 4] <- signif(QA[1, 3] * 100 / QA[1, 2], 2)
} else {
# Use raw response for ecotox
expdata$response <- expdata$raw_response
if (nlevels(expdata$type) > 1) {
message("There are data for more than one type of raw response in your data.\n",
"The types are ", paste(levels(expdata$type), collapse = " and "), ".\n",
"You should choose one of these types using 'endpoint = \"$type\"'",
"in your call to checkexperiment\n",
"For now, we are continuing with the data for ", levels(expdata$type)[1])
}
endpoint <- expdata$type[1]
expdata <- subset(expdata, type == endpoint)
controls <- subset(expdata, conc == 0)
expdata <- subset(expdata, conc != 0)
QA <- matrix(nrow = 1, ncol = 4,
dimnames = list(c("Control (conc = 0)"),
c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
}
numberOfControls <- length(controls$response)
QA["Control (conc = 0)", 1] <- numberOfControls
if (numberOfControls > 0) {
QA["Control (conc = 0)", 2] <- signif(mean(controls$response),2)
QA["Control (conc = 0)", 3] <- signif(sd(controls$response),2)
QA["Control (conc = 0)", 4] <- signif(QA["Control (conc = 0)", 3] * 100 /
QA["Control (conc = 0)", 2],2)
}
if (db == "ecotox") {
if (identical(as.character(levels(expdata$organism)), "Vibrio fischeri")) {
positive <- subset(expdata, substance == "Na Cl")
if (nrow(positive) > 0) {
QA <- rbind(QA,
c(nrow(positive),
signif(mean(positive$raw_response), 2),
signif(sd(positive$raw_response), 2),
signif(100 * sd(positive$raw_response) /
mean(positive$raw_response), 2)))
rownames(QA) <- c("Control (conc = 0)",
"Positive control (Na Cl)")
}
expdata <- subset(expdata, substance != "Na Cl", drop = TRUE)
}
}
if (length(expdata$experimentator) < 1) {
stop("There is no response data for ", exptype, " ",
id, " in database ", db, "\n")
}
exptypestring <- paste0(toupper(substring(exptype, 1, 1)),
substring(exptype, 2))
expdata$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)
# Info on the experiment
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$unit),"\n",
"\tComment:\t\t",comment,"\n",
"\tOK Levels:\t\t",levels(expdata$ok),"\n\n")
print(QA)
# Control growth rate for Lemna and algae
if (endpoint %in% c("cell count", "frond area", "frond number")) {
duration <- as.numeric(unique(expdata$duration)) # in hours
if (length(duration) > 1) stop("More than one duration in the data")
response_0 <- unique(expdata$raw_0)
if (length(response_0) > 1) stop("More than one mean response at time 0 in the data")
t_days <- duration / 24
control_growth_rates <- (log(controls$response) - log(response_0)) / t_days
cat("\nMean growth rate in controls:\t", round(mean(control_growth_rates), 3), "per day\n")
}
# Box plot of control data
if (db == "ecotox") {
boxplot(controls$response,
names="controls",
ylab=endpoint,
ylim=range(controls$response, na.rm = TRUE),
boxwex=0.4,
main=paste("Plate ",id))
} else {
boxplot(blinds$response,controls$response,
names=c("blinds","controls"),
ylab="Response",
boxwex=0.4,
main=paste("Plate ",id))
}
# Plot of dose response data
drdata <- expdata[c(2,4,6)]
drdata$substance <- factor(drdata$substance)
substances <- levels(drdata$substance)
lld <- log10(min(subset(drdata,conc!=0)$conc))
lhd <- log10(max(drdata$conc))
ylab <- if (db == "ecotox") endpoint else responsename
plot(1,type="n",
xlim = c(lld - 0.5, lhd + 2),
ylim = range(expdata[responsename], na.rm = TRUE),
xlab = paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
ylab = ylab)
drdatalist <- split(drdata,drdata$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)))
}
