From d12771d9fd5fa73be38bd247ec79043652f0d64c Mon Sep 17 00:00:00 2001 From: ranke Date: Fri, 21 Apr 2006 15:18:10 +0000 Subject: First chunk of work for making checkplate an alias to checkexperiment which will also work for the ecotox database. git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@65 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- R/checkexperiment.R | 101 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 101 insertions(+) create mode 100644 R/checkexperiment.R diff --git a/R/checkexperiment.R b/R/checkexperiment.R new file mode 100644 index 0000000..68169c7 --- /dev/null +++ b/R/checkexperiment.R @@ -0,0 +1,101 @@ +checkexperiment <- function(id,db="cytotox") +{ + 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) + + if (db %in% c("cytotox","enzymes")) { + blinds <- subset(controldata,type=="blind") + controls <- subset(controldata,type=="control") + + numberOfBlinds <- length(blinds$response) + stdOfBlinds <- sd(blinds$response) + } else { + controls <- subset(expdata,conc == 0) + + numberOfBlinds <- NA + stdOfBlinds <- 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$substance <- factor(expdata$substance) + expdata$unit <- factor(expdata$unit) + expdata$performed <- factor(expdata$performed) + expdata$ok <- factor(expdata$ok) + + numberOfControls <- length(controls$response) + + meanOfBlinds <- mean(blinds$response) + meanOfControls <- mean(controls$response) + stdOfControls <- sd(controls$response) + percentstdOfcontrols <-stdOfControls *100/meanOfControls + + cat("Plate ",plate," from database ",db,"\n", + "\tExperimentator: ",levels(platedata$experimentator),"\n", + "\tType(s): ",levels(platedata$type),"\n", + "\tPerformed on : ",levels(platedata$performed),"\n", + "\tSubstance(s): ",levels(platedata$substance),"\n", + "\tConcentration unit: ",levels(platedata$unit),"\n", + "\tOK: ",levels(platedata$ok),"\n", + "\t\tNumber \tMean \t\tStandard Deviation \t% Standard Deviation \n", + "\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n", + "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",stdOfControls,"\t\t",percentstdOfcontrols,"\n") + + par(ask=TRUE) + + boxplot(blinds$response,controls$response, + names=c("blinds","controls"), + ylab="Response",main=paste("Plate ",plate)) + + drdata <- platedata[c(2,4,6)] + drdata$substance <- factor(drdata$substance) + substances <- levels(drdata$substance) + + plot(log10(drdata$conc),drdata$viability, + xlim=c(-2.5, 4.5), + ylim= c(-0.1, 2), + xlab=paste("decadic logarithm of the concentration in ",levels(platedata$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("topleft",substances, pch=1, col=1:length(substances), inset=0.05) + title(main=paste("Plate ",plate," - ", + levels(platedata$experimentator)," - ",levels(platedata$type))) +} -- cgit v1.2.1