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

1 files changed, 101 insertions, 0 deletions

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)))
+}