From 2c5a4d04e567deb2fd97c4e0b1014fb82a15a6b8 Mon Sep 17 00:00:00 2001
From: "(no author)" <(no author)@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>
Date: Wed, 8 Sep 2004 12:18:15 +0000
Subject: Added the checkplate function.

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@5 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
---
 R/drfit.R | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 70 insertions(+), 2 deletions(-)

(limited to 'R')

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)))
+    }
+}
-- 
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