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-rw-r--r--R/checkplate.R81
1 files changed, 0 insertions, 81 deletions
diff --git a/R/checkplate.R b/R/checkplate.R
deleted file mode 100644
index 46afc53..0000000
--- a/R/checkplate.R
+++ /dev/null
@@ -1,81 +0,0 @@
-checkplate <- function(plate,db="cytotox")
-{
- library(RODBC)
- channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
-
- if (db == "cytotox") {
- responsetype <- "viability"
- testtype <- "celltype"
- } else {
- responsetype <- "activity"
- testtype <- "enzyme"
- }
-
- platequery <- paste("SELECT experimentator,substance,",testtype,",conc,unit,",responsetype,",performed,ok",
- "FROM ",db," WHERE plate=", plate)
-
- controlquery <- paste("SELECT type,response FROM controls WHERE plate=",plate)
-
- platedata <- sqlQuery(channel,platequery)
- controldata <- sqlQuery(channel,controlquery)
-
- odbcClose(channel)
-
- if (length(platedata$experimentator) < 1) {
- cat("There is no response data for plate ",plate," in database ",db,"\n")
- } else {
- platedata$experimentator <- factor(platedata$experimentator)
- platedata$type <- factor(platedata[[testtype]])
- platedata$substance <- factor(platedata$substance)
- platedata$unit <- factor(platedata$unit)
- platedata$performed <- factor(platedata$performed)
- platedata$ok <- factor(platedata$ok)
-
- blinds <- subset(controldata,type=="blind")
- controls <- subset(controldata,type=="control")
-
- numberOfBlinds <- length(blinds$response)
- numberOfControls <- length(controls$response)
- meanOfBlinds <- mean(blinds$response)
- meanOfControls <- mean(controls$response)
- stdOfBlinds <- sd(blinds$response)
- stdOfControls <- sd(controls$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)))
- }
-}

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