Added the checkplate function.

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@5 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

4 files changed, 106 insertions, 5 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 7ba2f92..07c87ef 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.02-4
-Date: 2004-08-31
+Version: 0.03-5
+Date: 2004-09-08
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/INDEX b/INDEX
index 52fea7c..f944eb1 100644
--- a/INDEX
+++ b/INDEX
@@ -1,5 +1,7 @@
 antifoul                Dose-Response data for TBT and Zink Pyrithione
                         in IPC-81 cells
+checkplate              Check raw data from a specified microtiter
+                        plate
 drdata                  Get dose-response data
 drfit                   Fit dose-response models
-drplot					Plot dose-response data and dose-response models
+drplot                  Plot dose-response models
diff --git a/R/drfit.R b/R/drfit.R
index a3b8a1b..cfc7263 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -3,7 +3,7 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
     ok="'ok'")

 {

     library(RODBC) 

-    cytotoxchannel <- odbcConnect("cytotox",uid="cytotox",pwd="cytotox",case="tolower")

+    channel <- odbcConnect("cytotox",uid="cytotox",pwd="cytotox",case="tolower")

     slist <- paste(substances,collapse="','")

     query <- paste("SELECT conc,viability,unit,experimentator,substance,celltype,",

         "plate,ok FROM cytotox WHERE substance IN ('",

@@ -12,7 +12,7 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
         celltype,"' AND ",

         whereClause," AND ok in (",

         ok,")",sep="")

-    data <- sqlQuery(cytotoxchannel,query)

+    data <- sqlQuery(channel,query)

     names(data)[[1]] <- "dose"

     names(data)[[2]] <- "response"

     data$dosefactor <- factor(data$dose)

@@ -367,3 +367,71 @@ drplot <- function(drresults, data = FALSE, dtype = "std", alpha = 0.95,
         }

     }

 }

+

+checkplate <- function(plate,db="cytotox") {

+    library(RODBC) 

+    channel <- odbcConnect(db,uid=db,pwd=db,case="tolower")

+

+    platequery <- paste("SELECT experimentator,substance,celltype,conc,unit,viability,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)

+

+    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$celltype <- factor(platedata$celltype)

+        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)

+        

+        cat("Plate ",plate," from database ",db,"\n",

+            "\tExperimentator: ",levels(platedata$experimentator),"\n",

+            "\tCell type(s): ",levels(platedata$celltype),"\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 \tStandard Deviation\n",

+            "blind\t\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",

+            "control\t",numberOfControls,"\t",meanOfControls,"\t",stdOfControls,"\n")

+        

+        par(ask=TRUE)

+        

+        boxplot(blinds$response,controls$response,names=c("blinds","controls"),ylab="Response",main=paste("Plate ",plate))

+        

+        drdata <- subset(platedata,select=c(substance,conc,viability))

+        drdata$substance <- factor(drdata$substance)

+        substances <- levels(drdata$substance)

+        substances

+       

+        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="Viability")

+        

+        drdatalist <- split(drdata,drdata$substance)

+        

+        for (i in 1:length(drdatalist)) {

+            points(log10(drdatalist[[i]]$conc),drdatalist[[i]]$viability,col=i);

+        }

+

+        legend(3.0,1.5,substances, pch=1, col=1:length(substances))

+        title(main=paste("Plate ",plate," - ",levels(platedata$experimentator)," - ",levels(platedata$celltype)))

+    }

+}

diff --git a/man/checkplate.Rd b/man/checkplate.Rd
new file mode 100644
index 0000000..43dcaac
--- /dev/null
+++ b/man/checkplate.Rd
@@ -0,0 +1,31 @@
+\name{checkplate}
+\alias{checkplate}
+\title{Check raw data from a specified microtiter plate}
+\description{
+  Report metadata from a specified microtiter plate from a specified database, box 
+  plot positive and negative (blind) controls, and show the response data on the 
+  plate.
+}
+\usage{
+  checkplate(plate,db="cytotox")
+}
+\arguments{
+  \item{plate}{
+    The number of the plate identifying it within the database.}
+  \item{db}{
+    The database to be used. Currently only "cytotox" of the UFT Department of
+    Bioorganic Chemistry is supported.}
+}
+\value{
+  The function lists a report and shows two graphs.
+}
+\examples{
+# Check plate number 1 in the cytotox database
+\dontrun{data <- checkplate(1)}
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{database}