I added the possibility to explicitly position or exclude the

legend(s).



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@19 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

4 files changed, 538 insertions, 527 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 25a9319..b5fed66 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.03-17
-Date: 2005-02-25
+Version: 0.03-19
+Date: 2005-03-14
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/drfit.R b/R/drfit.R
index 7ffb1a0..bc0bddd 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -1,521 +1,530 @@
-drdata <- function(substances, experimentator = "%", db = "cytotox",

-    celltype="IPC-81",enzymetype="AChE",whereClause="1",

-    ok="'ok'")

-{

-    library(RODBC) 

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

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

-    if (db == "cytotox") {

-        responsetype <- "viability"

-        testtype <- "celltype"

-        type <- celltype

-    } else {

-        responsetype <- "activity"

-        testtype <- "enzyme"

-        type <- enzymetype

-    }

-        

-    query <- paste("SELECT conc,",responsetype,",unit,experimentator,substance,",testtype,

-        ",plate,ok FROM ", db, " WHERE substance IN ('",

-        slist,"') AND experimentator LIKE '",

-        experimentator,"' AND ",testtype," LIKE '",

-        type,"' AND ",

-        whereClause," AND ok in (",

-        ok,")",sep="")

-    data <- sqlQuery(channel,query)

-    odbcClose(channel)

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

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

-    data$dosefactor <- factor(data$dose)

-    data$substance <- factor(data$substance,levels=substances)

-    return(data)

-}

-    

-linearlogisf <- function(x,k,f,mu,b)

-{

-    k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b)))

-}

-

-drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,

-        lognorm = TRUE, logis = FALSE,

-        linearlogis = FALSE, linearlogisWrong = NA, 

-        b0 = 2, f0 = 0)

-{

-    substances <- levels(data$substance)

-    unit <- levels(as.factor(data$unit))

-

-    ri <- rix <- 0                        # ri is the index over the result rows

-                                          # rix is used later to check if any

-                                          # model result was appended

-    rsubstance <- array()                 # the substance names in the results

-    rn <- vector()                        # number of dose-response curves 

-    rlhd <- rlld <- vector()              # highest and lowest doses tested

-    mtype <- array()                      # the modeltypes

-    sigma <- array()                      # the standard deviation of the residuals

-    logEC50 <- vector()

-    stderrlogEC50 <- vector()

-    slope <- vector()

-    b <- vector()

-    f <- vector()

-

-    splitted <- split(data,data$substance)

-    for (i in substances) {

-        tmp <- splitted[[i]]

-        fit <- FALSE

-        n <- round(length(tmp$response)/9)

-        if (length(tmp$response) == 0) {

-            nodata = TRUE

-        } else {

-            nodata = FALSE

-        }

-        rix <- ri

-        if (!nodata) {

-            if (is.na(startlogEC50[i])){

-                w <- 1/abs(tmp$response - 0.3)

-                startlogEC50[[i]] <- sum(w * log10(tmp$dose))/sum(w)

-            }

-            highestdose <- max(tmp$dose)

-            lowestdose <- min(tmp$dose)

-            lhd <- log10(highestdose)

-            lld <- log10(lowestdose)

-            responseathighestdose <- mean(subset(tmp,dose==highestdose)$response)

-            if (responseathighestdose < 0.5) {

-                inactive <- FALSE

-

-                if (linearlogis && 

-                    length(subset(linearlogisWrong,linearlogisWrong == i))==0) {

-                    m <- try(nls(response ~ linearlogisf(dose,1,f,logEC50,b),

-                            data=tmp,

-                            start=list(f=f0,logEC50=startlogEC50[[i]],b=b0)))

-                    if (!inherits(m, "try-error")) {

-                        fit <- TRUE

-                        ri <- ri + 1

-                        s <- summary(m)

-                        sigma[[ri]] <- s$sigma

-                        rsubstance[[ri]] <- i

-                        rn[[ri]] <- n

-                        rlld[[ri]] <- log10(lowestdose)

-                        rlhd[[ri]] <- log10(highestdose)

-                        mtype[[ri]] <- "linearlogis"

-                        logEC50[[ri]] <- coef(m)[["logEC50"]]

-                        slope[[ri]] <- NA

-                        if (logEC50[[ri]] > rlhd[[ri]]) {

-                            logEC50[[ri]] <- NA

-                            stderrlogEC50[[ri]] <- NA

-                            b[[ri]] <- NA

-                            f[[ri]] <- NA

-                        } else {

-                            stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]

-                            b[[ri]] <- coef(m)[["b"]]

-                            f[[ri]] <- coef(m)[["f"]]

-                        }

-                    }

-                }

-

-                if (logis) {

-                    m <- try(nls(response ~ plogis(-log10(dose),-logEC50,slope),

-                            data=tmp,

-                            start=list(logEC50=startlogEC50[[i]],slope=1)))

-                    if (chooseone==FALSE || fit==FALSE) {

-                        if (!inherits(m, "try-error")) {

-                            fit <- TRUE

-                            ri <- ri + 1

-                            s <- summary(m)

-                            sigma[[ri]] <- s$sigma

-                            rsubstance[[ri]] <- i

-                            rn[[ri]] <- n

-                            rlld[[ri]] <- log10(lowestdose)

-                            rlhd[[ri]] <- log10(highestdose)

-                            mtype[[ri]] <- "logis"

-                            logEC50[[ri]] <- coef(m)[["logEC50"]]

-                            b[[ri]] <- NA

-                            f[[ri]] <- NA

-                            if (logEC50[[ri]] > rlhd[[ri]]) {

-                                logEC50[[ri]] <- NA

-                                slope[[ri]] <- NA

-                                stderrlogEC50[[ri]] <- NA

-                            } else {

-                                slope[[ri]] <- coef(m)[["slope"]]

-                                stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]

-                            }

-                        }

-                    }

-                }

-

-                if (lognorm) {

-                    m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,slope),

-                                data=tmp,

-                                start=list(logEC50=startlogEC50[[i]],slope=1)))

-                    if (chooseone==FALSE || fit==FALSE) {

-                        if (!inherits(m, "try-error")) {

-                            fit <- TRUE

-                            ri <- ri + 1

-                            s <- summary(m)

-                            sigma[[ri]] <- s$sigma

-                            rsubstance[[ri]] <- i

-                            rn[[ri]] <- n

-                            rlld[[ri]] <- log10(lowestdose)

-                            rlhd[[ri]] <- log10(highestdose)

-                            mtype[[ri]] <- "lognorm"

-                            logEC50[[ri]] <- coef(m)[["logEC50"]]

-                            b[[ri]] <- NA

-                            f[[ri]] <- NA

-                            if (logEC50[[ri]] > rlhd[[ri]]) {

-                                logEC50[[ri]] <- NA

-                                slope[[ri]] <- NA

-                                stderrlogEC50[[ri]] <- NA

-                            } else {

-                                slope[[ri]] <- coef(m)[["slope"]]

-                                stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]

-                            }

-                        }

-                    }

-                }

-

-            } else {

-                inactive <- TRUE

-            }

-        }

-        if (ri == rix) {          # if no entry was appended for this substance

-            ri <- ri + 1

-            rsubstance[[ri]] <- i

-            rn[[ri]] <- n

-            if (nodata) {

-                rlld[[ri]] <- rlhd[[i]] <- NA

-                mtype[[ri]] <- "no data"

-            } else {

-                rlld[[ri]] <- log10(lowestdose)

-                rlhd[[i]] <- log10(highestdose)

-                if (inactive) {

-                    mtype[[ri]] <- "inactive"

-                } else {

-                    mtype[[ri]] <- "no fit"

-                }

-            }

-            sigma[[ri]] <- NA

-            logEC50[[ri]] <- NA

-            stderrlogEC50[[ri]] <- NA

-            slope[[ri]] <- NA

-            b[[ri]] <- NA

-            f[[ri]] <- NA

-        }

-    }

-    results <- data.frame(rsubstance,rn, rlhd, mtype, logEC50, stderrlogEC50, unit, sigma)

-    names(results) <- c("Substance","n", "lhd","mtype","logEC50","std","unit","sigma")

-    if (lognorm || logis) {

-        results$slope <- slope

-    }

-    if (linearlogis) {

-        results$b <- b

-        results$f <- f

-    }

-    return(results)

-}

-

-drplot <- function(drresults, data, dtype = "std", alpha = 0.95,

-        path = "./", fileprefix = "drplot", overlay = FALSE,

-        postscript = FALSE, png = FALSE, bw = TRUE,

-        colors = 1:8,devoff=T)

-{

-    unitlevels <- levels(as.factor(drresults$unit))

-    if (length(unitlevels) == 1) {

-        unit <- unitlevels

-    } else {

-        unit <- "different units"

-    }

-

-    # Get the plot limits on the x-axis (log of the dose)

-    if(is.data.frame(data)) {

-        if (min(data$dose == 0)) {

-            cat("At least one of the dose levels is 0 - this is not a valid dose.")

-        } else {

-            lld <- log10(min(data$dose))

-        }

-        lhd <- log10(max(data$dose))

-        hr <- max(data$response)

-        dsubstances <- levels(data$substance)    

-    } else {

-        lld <- min(drresults[["logEC50"]],na.rm=TRUE) - 2

-        lhd <- max(drresults[["logEC50"]],na.rm=TRUE) + 2

-        if (length(subset(drresults,mtype=="linearlogis")$Substance) != 0) {

-            hr <- 1.8 

-        } else {

-            hr <- 1.0

-        }

-    }

-

-    # Prepare overlay plot if requested

-    if (overlay)

-    {

-        if (postscript) {

-            filename = paste(path,fileprefix,".eps",sep="")

-            postscript(file=filename,

-                    paper="special",width=7,height=7,horizontal=FALSE,pointsize=12) 

-            cat("Created File: ",filename,"\n")

-        } 

-        if (png) {

-            filename = paste(path,fileprefix,".png",sep="")

-            png(filename=filename,

-                width=500, height=500,pointsize=12)

-            cat("Created File: ",filename,"\n")

-        }

-        if (!postscript && !png) {

-            x11(width=7,height=7,pointsize=12)

-        }

-            

-        plot(0,type="n",

-            xlim=c(lld - 0.5, lhd + 1),

-            ylim= c(-0.1, hr + 0.2),

-            xlab=paste("Decadic Logarithm of the dose in ", unit),    

-            ylab="Normalized response")

-    }

-

-    # Plot the data either as raw data or as error bars

-    if(is.data.frame(data)) {

-        splitted <- split(data,data$substance)

-        n <- 0

-        if (bw) colors <- rep("black",length(dsubstances))

-        for (i in dsubstances) {

-            n <- n + 1

-            tmp <- splitted[[i]]

-            if (length(tmp$response) != 0) {

-                color <- colors[[n]]

-                # Prepare the single graphs if an overlay is not requested

-                if (!overlay)

-                {

-                    if (postscript) {

-                        filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".eps",sep="")

-                        postscript(file=filename,

-                                paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)

-                        cat("Created File: ",filename,"\n")

-                    } 

-                    if (png) {

-                        filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".png",sep="")

-                        png(filename=filename,

-                            width=500, height=500,pointsize=12)

-                        cat("Created File: ",filename,"\n")

-                    }

-                    if (!postscript && !png) {

-                        x11(width=7,height=7,pointsize=12)

-                    }

-                        

-                    plot(0,type="n",

-                        xlim=c(lld - 0.5, lhd + 2),

-                        ylim= c(-0.1, hr + 0.2),

-                        xlab=paste("Decadic Logarithm of the dose in ", unit),    

-                        ylab="Normalized response")

-                }

-                if (!overlay) legend(lhd - 1, hr + 0.1, i,lty = 1, col = color)

-                tmp$dosefactor <- factor(tmp$dose)  # necessary because the old

-                                                    # factor has all levels, not 

-                                                    # only the ones tested with

-                                                    # this substance

-                # Plot the data, if requested

-                if (dtype != "none") {

-                    if (dtype == "raw") {

-                        points(log10(tmp$dose),tmp$response,col=color)

-                    } else {

-                        splitresponses <- split(tmp$response,tmp$dosefactor)

-                        means <- sapply(splitresponses,mean)

-                        lengths <- sapply(splitresponses,length)

-                        vars <- sapply(splitresponses,var)

-                        standarddeviations <- sqrt(vars)

-                    }

-                    if (dtype == "std")

-                    {

-                        tops <- means + standarddeviations

-                        bottoms <- means - standarddeviations

-                    }

-                    if (dtype == "conf")

-                    {

-                        confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) 

-                        tops <- means + confidencedeltas

-                        bottoms <- means - confidencedeltas

-                    }

-                    if (dtype != "raw")

-                    {

-                        x <- log10(as.numeric(levels(tmp$dosefactor)))

-                        segments(x,bottoms,x,tops,col=color)

-                        points(x,means,col=color)

-                        smidge <- 0.05

-                        segments(x - smidge,bottoms,x + smidge,bottoms,col=color)

-                        segments(x - smidge,tops,x + smidge,tops,col=color)

-                    }

-                }

-

-                # Plot the fits, if there are any

-                fits <- subset(drresults,Substance == i)

-                nf <-  length(fits$Substance)  # number of fits to plot

-                if (nf > 0) {

-                    for (j in 1:nf)

-                    {

-                        logEC50 <- fits[j,"logEC50"]

-                        mtype <- as.character(fits[j, "mtype"])

-                        if (mtype == "lognorm") {

-                            slope <- fits[j,"slope"]

-                            plot(function(x) pnorm(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)

-                        }

-                        if (mtype == "logis") {

-                            slope <- fits[j,"slope"]

-                            plot(function(x) plogis(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)

-                        }

-                        if (mtype == "linearlogis") {

-                            plot(function(x) linearlogisf(10^x,1,fits[j,"f"],fits[j,"logEC50"],fits[j,"b"]),

-                                lld - 0.5, lhd + 2,

-                                add=TRUE,col=color)

-                        }

-                    }

-                }

-                if (!overlay && (postscript || png)) dev.off()

-            } else {

-                cat("No data for ",i,"\n")

-            }

-        }

-    }

-    if (overlay) legend(lhd - 1, hr + 0.1, dsubstances,lty = 1, col = colors)

-    if (overlay && (postscript || png)) {

-        if (devoff) {

-            dev.off()

-        }

-    }

-}

-

-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)

-        

-        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 \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 <- 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(3.0,1.5,substances, pch=1, col=1:length(substances))

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

-    }

-}

-

-checksubstance <- function(substance,db="cytotox",experimentator="%",celltype="%",enzymetype="%",whereClause="1",ok="%") 

-{

-    library(RODBC) 

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

-

-    if (db == "cytotox") {

-        responsetype <- "viability"

-        testtype <- "celltype"

-        type <- celltype

-    } else {

-        responsetype <- "activity"

-        testtype <- "enzyme"

-        type <- enzymetype

-    }

-    query <- paste("SELECT experimentator,substance,",testtype,",plate,conc,unit,",responsetype,",ok",

-        " FROM ",db," WHERE substance LIKE '",

-        substance,"' AND experimentator LIKE '",

-        experimentator,"' AND ",testtype," LIKE '",

-        type,"' AND ",

-        whereClause," AND ok LIKE '",ok,"'",sep="")

-

-    data <- sqlQuery(channel,query)

-    odbcClose(channel)

-    

-    data$experimentator <- factor(data$experimentator)    

-    data$substance <- factor(data$substance)

-    substances <- levels(data$substance)    

-    data$type <- factor(data[[testtype]])                

-    data$plate <- factor(data$plate)                        

-    plates <- levels(data$plate)

-    concentrations <- split(data$conc,data$conc)

-    concentrations <- as.numeric(names(concentrations))

-    data$unit <- factor(data$unit)                        

-    data$ok <- factor(data$ok)

-    

-    if (length(plates)>6) {

-        palette(rainbow(length(plates)))      

-    }

- 

-    plot(log10(data$conc),data[[responsetype]],

-        xlim=c(-2.5, 4.5),                                                                  

-        ylim= c(-0.1, 2),                                                                 

-        xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),    

-        ylab=responsetype)  

-        

-    platelist <- split(data,data$plate)

-   

-    for (i in 1:length(platelist)) {    

-        points(log10(platelist[[i]]$conc),platelist[[i]][[responsetype]],col=i);          

-    }       

-    

-    legend(3.5,1.7,plates, pch=1, col=1:length(plates))

-    title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$type)))

- 

-    cat("Substanz ",substance,"\n",

-        "\tExperimentator(s):",levels(data$experimentator),"\n",

-        "\tType(s):\t",levels(data$type),"\n",

-        "\tSubstance(s):\t",levels(data$substance),"\n",

-        "\tPlate(s):\t",plates,"\n\n")

-}

+drdata <- function(substances, experimentator = "%", db = "cytotox",
+    celltype="IPC-81",enzymetype="AChE",whereClause="1",
+    ok="'ok'")
+{
+    library(RODBC) 
+    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+    slist <- paste(substances,collapse="','")
+    if (db == "cytotox") {
+        responsetype <- "viability"
+        testtype <- "celltype"
+        type <- celltype
+    } else {
+        responsetype <- "activity"
+        testtype <- "enzyme"
+        type <- enzymetype
+    }
+        
+    query <- paste("SELECT conc,",responsetype,",unit,experimentator,substance,",testtype,
+        ",plate,ok FROM ", db, " WHERE substance IN ('",
+        slist,"') AND experimentator LIKE '",
+        experimentator,"' AND ",testtype," LIKE '",
+        type,"' AND ",
+        whereClause," AND ok in (",
+        ok,")",sep="")
+    data <- sqlQuery(channel,query)
+    odbcClose(channel)
+    names(data)[[1]] <- "dose"
+    names(data)[[2]] <- "response"
+    data$dosefactor <- factor(data$dose)
+    data$substance <- factor(data$substance,levels=substances)
+    return(data)
+}
+    
+linearlogisf <- function(x,k,f,mu,b)
+{
+    k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b)))
+}
+
+drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
+        lognorm = TRUE, logis = FALSE,
+        linearlogis = FALSE, linearlogisWrong = NA, 
+        b0 = 2, f0 = 0)
+{
+    substances <- levels(data$substance)
+    unit <- levels(as.factor(data$unit))
+
+    ri <- rix <- 0                        # ri is the index over the result rows
+                                          # rix is used later to check if any
+                                          # model result was appended
+    rsubstance <- array()                 # the substance names in the results
+    rn <- vector()                        # number of dose-response curves 
+    rlhd <- rlld <- vector()              # highest and lowest doses tested
+    mtype <- array()                      # the modeltypes
+    sigma <- array()                      # the standard deviation of the residuals
+    logEC50 <- vector()
+    stderrlogEC50 <- vector()
+    slope <- vector()
+    b <- vector()
+    f <- vector()
+
+    splitted <- split(data,data$substance)
+    for (i in substances) {
+        tmp <- splitted[[i]]
+        fit <- FALSE
+        n <- round(length(tmp$response)/9)
+        if (length(tmp$response) == 0) {
+            nodata = TRUE
+        } else {
+            nodata = FALSE
+        }
+        rix <- ri
+        if (!nodata) {
+            if (is.na(startlogEC50[i])){
+                w <- 1/abs(tmp$response - 0.3)
+                startlogEC50[[i]] <- sum(w * log10(tmp$dose))/sum(w)
+            }
+            highestdose <- max(tmp$dose)
+            lowestdose <- min(tmp$dose)
+            lhd <- log10(highestdose)
+            lld <- log10(lowestdose)
+            responseathighestdose <- mean(subset(tmp,dose==highestdose)$response)
+            if (responseathighestdose < 0.5) {
+                inactive <- FALSE
+
+                if (linearlogis && 
+                    length(subset(linearlogisWrong,linearlogisWrong == i))==0) {
+                    m <- try(nls(response ~ linearlogisf(dose,1,f,logEC50,b),
+                            data=tmp,
+                            start=list(f=f0,logEC50=startlogEC50[[i]],b=b0)))
+                    if (!inherits(m, "try-error")) {
+                        fit <- TRUE
+                        ri <- ri + 1
+                        s <- summary(m)
+                        sigma[[ri]] <- s$sigma
+                        rsubstance[[ri]] <- i
+                        rn[[ri]] <- n
+                        rlld[[ri]] <- log10(lowestdose)
+                        rlhd[[ri]] <- log10(highestdose)
+                        mtype[[ri]] <- "linearlogis"
+                        logEC50[[ri]] <- coef(m)[["logEC50"]]
+                        slope[[ri]] <- NA
+                        if (logEC50[[ri]] > rlhd[[ri]]) {
+                            logEC50[[ri]] <- NA
+                            stderrlogEC50[[ri]] <- NA
+                            b[[ri]] <- NA
+                            f[[ri]] <- NA
+                        } else {
+                            stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+                            b[[ri]] <- coef(m)[["b"]]
+                            f[[ri]] <- coef(m)[["f"]]
+                        }
+                    }
+                }
+
+                if (logis) {
+                    m <- try(nls(response ~ plogis(-log10(dose),-logEC50,slope),
+                            data=tmp,
+                            start=list(logEC50=startlogEC50[[i]],slope=1)))
+                    if (chooseone==FALSE || fit==FALSE) {
+                        if (!inherits(m, "try-error")) {
+                            fit <- TRUE
+                            ri <- ri + 1
+                            s <- summary(m)
+                            sigma[[ri]] <- s$sigma
+                            rsubstance[[ri]] <- i
+                            rn[[ri]] <- n
+                            rlld[[ri]] <- log10(lowestdose)
+                            rlhd[[ri]] <- log10(highestdose)
+                            mtype[[ri]] <- "logis"
+                            logEC50[[ri]] <- coef(m)[["logEC50"]]
+                            b[[ri]] <- NA
+                            f[[ri]] <- NA
+                            if (logEC50[[ri]] > rlhd[[ri]]) {
+                                logEC50[[ri]] <- NA
+                                slope[[ri]] <- NA
+                                stderrlogEC50[[ri]] <- NA
+                            } else {
+                                slope[[ri]] <- coef(m)[["slope"]]
+                                stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+                            }
+                        }
+                    }
+                }
+
+                if (lognorm) {
+                    m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,slope),
+                                data=tmp,
+                                start=list(logEC50=startlogEC50[[i]],slope=1)))
+                    if (chooseone==FALSE || fit==FALSE) {
+                        if (!inherits(m, "try-error")) {
+                            fit <- TRUE
+                            ri <- ri + 1
+                            s <- summary(m)
+                            sigma[[ri]] <- s$sigma
+                            rsubstance[[ri]] <- i
+                            rn[[ri]] <- n
+                            rlld[[ri]] <- log10(lowestdose)
+                            rlhd[[ri]] <- log10(highestdose)
+                            mtype[[ri]] <- "lognorm"
+                            logEC50[[ri]] <- coef(m)[["logEC50"]]
+                            b[[ri]] <- NA
+                            f[[ri]] <- NA
+                            if (logEC50[[ri]] > rlhd[[ri]]) {
+                                logEC50[[ri]] <- NA
+                                slope[[ri]] <- NA
+                                stderrlogEC50[[ri]] <- NA
+                            } else {
+                                slope[[ri]] <- coef(m)[["slope"]]
+                                stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+                            }
+                        }
+                    }
+                }
+
+            } else {
+                inactive <- TRUE
+            }
+        }
+        if (ri == rix) {          # if no entry was appended for this substance
+            ri <- ri + 1
+            rsubstance[[ri]] <- i
+            rn[[ri]] <- n
+            if (nodata) {
+                rlld[[ri]] <- rlhd[[i]] <- NA
+                mtype[[ri]] <- "no data"
+            } else {
+                rlld[[ri]] <- log10(lowestdose)
+                rlhd[[i]] <- log10(highestdose)
+                if (inactive) {
+                    mtype[[ri]] <- "inactive"
+                } else {
+                    mtype[[ri]] <- "no fit"
+                }
+            }
+            sigma[[ri]] <- NA
+            logEC50[[ri]] <- NA
+            stderrlogEC50[[ri]] <- NA
+            slope[[ri]] <- NA
+            b[[ri]] <- NA
+            f[[ri]] <- NA
+        }
+    }
+    results <- data.frame(rsubstance,rn, rlhd, mtype, logEC50, stderrlogEC50, unit, sigma)
+    names(results) <- c("Substance","n", "lhd","mtype","logEC50","std","unit","sigma")
+    if (lognorm || logis) {
+        results$slope <- slope
+    }
+    if (linearlogis) {
+        results$b <- b
+        results$f <- f
+    }
+    return(results)
+}
+
+drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
+        path = "./", fileprefix = "drplot", overlay = FALSE,
+        postscript = FALSE, png = FALSE, bw = TRUE,
+        colors = 1:8,devoff=T,lpos=FALSE)
+{
+    unitlevels <- levels(as.factor(drresults$unit))
+    if (length(unitlevels) == 1) {
+        unit <- unitlevels
+    } else {
+        unit <- "different units"
+    }
+
+    # Get the plot limits on the x-axis (log of the dose)
+    if(is.data.frame(data)) {
+        if (min(data$dose == 0)) {
+            cat("At least one of the dose levels is 0 - this is not a valid dose.")
+        } else {
+            lld <- log10(min(data$dose))
+        }
+        lhd <- log10(max(data$dose))
+        hr <- max(data$response)
+        dsubstances <- levels(data$substance)    
+    } else {
+        lld <- min(drresults[["logEC50"]],na.rm=TRUE) - 2
+        lhd <- max(drresults[["logEC50"]],na.rm=TRUE) + 2
+        if (length(subset(drresults,mtype=="linearlogis")$Substance) != 0) {
+            hr <- 1.8 
+        } else {
+            hr <- 1.0
+        }
+    }
+
+    # Legend position
+    if (!lpos[[1]]) {
+        lx <- lhd - 1
+        ly <- hr + 0.1
+    } else {
+        lx <- lpos[[1]]
+        ly <- lpos[[2]]
+    }
+
+    # Prepare overlay plot if requested
+    if (overlay)
+    {
+        if (postscript) {
+            filename = paste(path,fileprefix,".eps",sep="")
+            postscript(file=filename,
+                    paper="special",width=7,height=7,horizontal=FALSE,pointsize=12) 
+            cat("Created File: ",filename,"\n")
+        } 
+        if (png) {
+            filename = paste(path,fileprefix,".png",sep="")
+            png(filename=filename,
+                width=500, height=500,pointsize=12)
+            cat("Created File: ",filename,"\n")
+        }
+        if (!postscript && !png) {
+            x11(width=7,height=7,pointsize=12)
+        }
+            
+        plot(0,type="n",
+            xlim=c(lld - 0.5, lhd + 1),
+            ylim= c(-0.1, hr + 0.2),
+            xlab=paste("Decadic Logarithm of the dose in ", unit),    
+            ylab="Normalized response")
+    }
+
+    # Plot the data either as raw data or as error bars
+    if(is.data.frame(data)) {
+        splitted <- split(data,data$substance)
+        n <- 0
+        if (bw) colors <- rep("black",length(dsubstances))
+        for (i in dsubstances) {
+            n <- n + 1
+            tmp <- splitted[[i]]
+            if (length(tmp$response) != 0) {
+                color <- colors[[n]]
+                # Prepare the single graphs if an overlay is not requested
+                if (!overlay)
+                {
+                    if (postscript) {
+                        filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".eps",sep="")
+                        postscript(file=filename,
+                                paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)
+                        cat("Created File: ",filename,"\n")
+                    } 
+                    if (png) {
+                        filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".png",sep="")
+                        png(filename=filename,
+                            width=500, height=500,pointsize=12)
+                        cat("Created File: ",filename,"\n")
+                    }
+                    if (!postscript && !png) {
+                        x11(width=7,height=7,pointsize=12)
+                    }
+                        
+                    plot(0,type="n",
+                        xlim=c(lld - 0.5, lhd + 2),
+                        ylim= c(-0.1, hr + 0.2),
+                        xlab=paste("Decadic Logarithm of the dose in ", unit),    
+                        ylab="Normalized response")
+                }
+                if (!overlay) legend(lx, ly, i,lty = 1, col = color)
+                tmp$dosefactor <- factor(tmp$dose)  # necessary because the old
+                                                    # factor has all levels, not 
+                                                    # only the ones tested with
+                                                    # this substance
+                # Plot the data, if requested
+                if (dtype != "none") {
+                    if (dtype == "raw") {
+                        points(log10(tmp$dose),tmp$response,col=color)
+                    } else {
+                        splitresponses <- split(tmp$response,tmp$dosefactor)
+                        means <- sapply(splitresponses,mean)
+                        lengths <- sapply(splitresponses,length)
+                        vars <- sapply(splitresponses,var)
+                        standarddeviations <- sqrt(vars)
+                    }
+                    if (dtype == "std")
+                    {
+                        tops <- means + standarddeviations
+                        bottoms <- means - standarddeviations
+                    }
+                    if (dtype == "conf")
+                    {
+                        confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) 
+                        tops <- means + confidencedeltas
+                        bottoms <- means - confidencedeltas
+                    }
+                    if (dtype != "raw")
+                    {
+                        x <- log10(as.numeric(levels(tmp$dosefactor)))
+                        segments(x,bottoms,x,tops,col=color)
+                        points(x,means,col=color)
+                        smidge <- 0.05
+                        segments(x - smidge,bottoms,x + smidge,bottoms,col=color)
+                        segments(x - smidge,tops,x + smidge,tops,col=color)
+                    }
+                }
+
+                # Plot the fits, if there are any
+                fits <- subset(drresults,Substance == i)
+                nf <-  length(fits$Substance)  # number of fits to plot
+                if (nf > 0) {
+                    for (j in 1:nf)
+                    {
+                        logEC50 <- fits[j,"logEC50"]
+                        mtype <- as.character(fits[j, "mtype"])
+                        if (mtype == "lognorm") {
+                            slope <- fits[j,"slope"]
+                            plot(function(x) pnorm(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)
+                        }
+                        if (mtype == "logis") {
+                            slope <- fits[j,"slope"]
+                            plot(function(x) plogis(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)
+                        }
+                        if (mtype == "linearlogis") {
+                            plot(function(x) linearlogisf(10^x,1,fits[j,"f"],fits[j,"logEC50"],fits[j,"b"]),
+                                lld - 0.5, lhd + 2,
+                                add=TRUE,col=color)
+                        }
+                    }
+                }
+                if (!overlay && (postscript || png)) dev.off()
+            } else {
+                cat("No data for ",i,"\n")
+            }
+        }
+    }
+    if (overlay) legend(lx, ly, dsubstances,lty = 1, col = colors)
+    if (overlay && (postscript || png)) {
+        if (devoff) {
+            dev.off()
+        }
+    }
+}
+
+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)
+        
+        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 \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 <- 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(3.0,1.5,substances, pch=1, col=1:length(substances))
+        title(main=paste("Plate ",plate," - ",levels(platedata$experimentator)," - ",levels(platedata$type)))
+    }
+}
+
+checksubstance <- function(substance,db="cytotox",experimentator="%",celltype="%",enzymetype="%",whereClause="1",ok="%") 
+{
+    library(RODBC) 
+    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+
+    if (db == "cytotox") {
+        responsetype <- "viability"
+        testtype <- "celltype"
+        type <- celltype
+    } else {
+        responsetype <- "activity"
+        testtype <- "enzyme"
+        type <- enzymetype
+    }
+    query <- paste("SELECT experimentator,substance,",testtype,",plate,conc,unit,",responsetype,",ok",
+        " FROM ",db," WHERE substance LIKE '",
+        substance,"' AND experimentator LIKE '",
+        experimentator,"' AND ",testtype," LIKE '",
+        type,"' AND ",
+        whereClause," AND ok LIKE '",ok,"'",sep="")
+
+    data <- sqlQuery(channel,query)
+    odbcClose(channel)
+    
+    data$experimentator <- factor(data$experimentator)    
+    data$substance <- factor(data$substance)
+    substances <- levels(data$substance)    
+    data$type <- factor(data[[testtype]])                
+    data$plate <- factor(data$plate)                        
+    plates <- levels(data$plate)
+    concentrations <- split(data$conc,data$conc)
+    concentrations <- as.numeric(names(concentrations))
+    data$unit <- factor(data$unit)                        
+    data$ok <- factor(data$ok)
+    
+    if (length(plates)>6) {
+        palette(rainbow(length(plates)))      
+    }
+ 
+    plot(log10(data$conc),data[[responsetype]],
+        xlim=c(-2.5, 4.5),                                                                  
+        ylim= c(-0.1, 2),                                                                 
+        xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),    
+        ylab=responsetype)  
+        
+    platelist <- split(data,data$plate)
+   
+    for (i in 1:length(platelist)) {    
+        points(log10(platelist[[i]]$conc),platelist[[i]][[responsetype]],col=i);          
+    }       
+    
+    legend(3.5,1.7,plates, pch=1, col=1:length(plates))
+    title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$type)))
+ 
+    cat("Substanz ",substance,"\n",
+        "\tExperimentator(s):",levels(data$experimentator),"\n",
+        "\tType(s):\t",levels(data$type),"\n",
+        "\tSubstance(s):\t",levels(data$substance),"\n",
+        "\tPlate(s):\t",plates,"\n\n")
+}
diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd
index e9915e7..194688a 100644
--- a/man/checksubstance.Rd
+++ b/man/checksubstance.Rd
@@ -6,7 +6,7 @@
   the data.
 }
 \usage{
-  checksubstance(substance,db="cytotox",experimentator="%",celltype="%",whereClause="1",ok="%")
+  checksubstance(substance,db="cytotox",experimentator="\%",celltype="\%",whereClause="1",ok="%")
 }
 \arguments{
   \item{substance}{
@@ -20,9 +20,9 @@
     means that data from all experimentators are shown.}
   \item{celltype}{
     Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.
-    Default is "\%", i.e. any cell type.}
+    Default is "\%", i.e. data for any cell type will be displayed.}
   \item{enzymetype}{
-    Currently, only data for AChE, GR and GST are supported.}
+    Currently, only data for AChE, GR and GST are supported. The default value is "\%", i.e. data for any enzyme type will be displayed.}
   \item{whereClause}{
     With this argument, additional conditions for the SQL query can be set, 
     e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).}
diff --git a/man/drplot.Rd b/man/drplot.Rd
index c9b1979..b162d45 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -7,7 +7,7 @@
 }
 \usage{
   drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
-    postscript, png, bw, colors, devoff)
+    postscript, png, bw, colors, devoff, lpos)
 }
 \arguments{
   \item{drresults}{
@@ -62,6 +62,8 @@
   \item{colors}{
     This is a vector of colors, defaulting to 1:8, used for plotting the data.
     }
+  \item{lpos}{
+    A optional vector with the x and y position of the upper left corner of the legend. The default guess is not always the optimum.}
   \item{devoff}{
     If set to FALSE, the closing of the device after creation of an overlay png
     or postscript graph will be left out, so texts and other elements can be