checkexperiment <- function(id,db="ecotox") { databases <- data.frame( responsetype=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 does not exist") library(RODBC) channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower") responsetype = as.character(databases[db,1]) testtype = as.character(databases[db,2]) exptype = as.character(databases[db,3]) expquery <- paste("SELECT experimentator,substance,", testtype,",conc,unit,",responsetype,",performed,ok", "FROM ",db," WHERE ",exptype,"=", id) expdata <- sqlQuery(channel,expquery) if (db %in% c("cytotox","enzymes")) { controlquery <- paste("SELECT type,response FROM controls WHERE plate=",id) controldata <- sqlQuery(channel,controlquery) } 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$experimentator) < 1) { stop("There is no response data for ",exptype," ", id," in database ",db,"\n") } expdata$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",exptype," ",id," from database ",db,"\n", "\tExperimentator(s): ",levels(expdata$experimentator),"\n", "\tType(s): ",levels(expdata$type),"\n", "\tPerformed on: ",levels(expdata$performed),"\n", "\tSubstance(s): ",levels(expdata$substance),"\n", "\tConcentration unit(s): ",levels(expdata$unit),"\n", "\tOK: ",levels(expdata$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=responsetype) drdatalist <- split(drdata,drdata$substance) for (i in 1:length(drdatalist)) { points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsetype]],col=i); } legend("topright",substances, pch=1, col=1:length(substances), inset=0.05) title(main=paste(levels(expdata$experimentator), " - ",levels(expdata$type))) }