1 files changed, 81 insertions, 0 deletions
diff --git a/R/checkplate.R b/R/checkplate.R
new file mode 100644
index 0000000..46afc53
--- /dev/null
+++ b/R/checkplate.R
@@ -0,0 +1,81 @@
+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)))
+    }
+}