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-rw-r--r--DESCRIPTION4
-rw-r--r--R/checkexperiment.R82
-rw-r--r--R/checkplate.R81
-rw-r--r--man/checkexperiment.Rd33
-rw-r--r--man/checkplate.Rd33
5 files changed, 85 insertions, 148 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 38039ae..788cc96 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: drfit
-Version: 0.05-63
-Date: 2006-04-06
+Version: 0.04-65
+Date: 2006-04-21
Title: Dose-response data evaluation
Author: Johannes Ranke <jranke@uni-bremen.de>
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 68169c7..c29b1e5 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -1,4 +1,4 @@
-checkexperiment <- function(id,db="cytotox")
+checkexperiment <- function(id,db="ecotox")
{
databases <- data.frame(
responsetype=c("viability","activity","response"),
@@ -34,15 +34,25 @@ checkexperiment <- function(id,db="cytotox")
controls <- subset(controldata,type=="control")
numberOfBlinds <- length(blinds$response)
- stdOfBlinds <- sd(blinds$response)
+ meanOfBlinds <- signif(mean(blinds$response),2)
+ stdOfBlinds <- signif(sd(blinds$response),2)
} else {
controls <- subset(expdata,conc == 0)
+ expdata <- subset(expdata, conc != 0)
numberOfBlinds <- NA
+ meanOfBlinds <- NA
stdOfBlinds <- NA
}
-
+ numberOfControls <- length(controls$response)
+ if (numberOfControls > 0) {
+ meanOfControls <- signif(mean(controls$response),2)
+ stdOfControls <- signif(sd(controls$response),2)
+ percentstdOfcontrols <-signif(stdOfControls *100/meanOfControls,2)
+ } else {
+ meanOfControls <- stdOfControls <- percentstdOfcontrols <- NA
+ }
if (length(expdata$experimentator) < 1) {
stop("There is no response data for ",exptype," ",
@@ -50,43 +60,51 @@ checkexperiment <- function(id,db="cytotox")
}
expdata$experimentator <- factor(expdata$experimentator)
expdata$type <- factor(expdata[[testtype]])
+ expdata$performed <- factor(as.character(expdata$performed))
expdata$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$ok),"\n",
- "\t\tNumber \tMean \t\tStandard Deviation \t% Standard Deviation \n",
+ cat("\n",exptype," ",id," from database ",db,"\n",
+ "\tExperimentator(s): ",levels(expdata$experimentator),"\n",
+ "\tType(s): ",levels(expdata$type),"\n",
+ "\tPerformed on: ",levels(expdata$performed),"\n",
+ "\tSubstance(s): ",levels(expdata$substance),"\n",
+ "\tConcentration unit(s): ",levels(expdata$unit),"\n",
+ "\tOK: ",levels(expdata$ok),"\n",
+ "\t\tNumber \tMean \tStd. Dev. \t% Std. Dev.\n",
"\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",
- "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",stdOfControls,"\t\t",percentstdOfcontrols,"\n")
+ "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",
+ stdOfControls,"\t\t",percentstdOfcontrols,"\n")
- par(ask=TRUE)
-
- boxplot(blinds$response,controls$response,
- names=c("blinds","controls"),
- ylab="Response",main=paste("Plate ",plate))
+ get(getOption("device"))(width=10,height=5)
+ par(mfcol=c(1,2))
+ if (db == "ecotox") {
+ boxplot(controls$response,
+ names="controls",
+ ylab="Response",
+ ylim=c(0,max(controls$response)),
+ boxwex=0.4,
+ main=paste("Plate ",id))
+ } else {
+ boxplot(blinds$response,controls$response,
+ names=c("blinds","controls"),
+ ylab="Response",
+ boxwex=0.4,
+ main=paste("Plate ",id))
+ }
- drdata <- platedata[c(2,4,6)]
+ drdata <- expdata[c(2,4,6)]
drdata$substance <- factor(drdata$substance)
substances <- levels(drdata$substance)
- plot(log10(drdata$conc),drdata$viability,
- xlim=c(-2.5, 4.5),
+ lld <- log10(min(subset(drdata,conc!=0)$conc))
+ lhd <- log10(max(drdata$conc))
+
+ plot(1,type="n",
+ xlim=c(lld - 0.5, lhd + 2),
ylim= c(-0.1, 2),
- xlab=paste("decadic logarithm of the concentration in ",levels(platedata$unit)),
+ xlab=paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
ylab=responsetype)
drdatalist <- split(drdata,drdata$substance)
@@ -95,7 +113,7 @@ checkexperiment <- function(id,db="cytotox")
points(log10(drdatalist[[i]]$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)))
+ legend("topright",substances, pch=1, col=1:length(substances), inset=0.05)
+ title(main=paste(levels(expdata$experimentator),
+ " - ",levels(expdata$type)))
}
diff --git a/R/checkplate.R b/R/checkplate.R
deleted file mode 100644
index 46afc53..0000000
--- a/R/checkplate.R
+++ /dev/null
@@ -1,81 +0,0 @@
-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)))
- }
-}
diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd
new file mode 100644
index 0000000..54352e8
--- /dev/null
+++ b/man/checkexperiment.Rd
@@ -0,0 +1,33 @@
+\name{checkexperiment}
+\alias{checkexperiment}
+\alias{checkplate}
+\title{Check raw data from a specified experiment or microtiter plate}
+\description{
+ Report metadata from a specified experiment or microtiter plate from a
+ specified database, box plot controls, and plot the dose-response data.
+}
+\usage{
+ checkplate(id,db="cytotox")
+ checkexperiment(id,db="ecotox")
+}
+\arguments{
+ \item{id}{
+ The id of the experiment or the plate identifying it within the database.}
+ \item{db}{
+ The database to be used. Currently, the microtiter plate databases
+ "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are
+ supported, as well as the database of ecotoxicity experiments "ecotox".}
+}
+\value{
+ The function lists a report and shows two graphs side by side.
+}
+\examples{
+# Check plate number 1 in the cytotox database
+\dontrun{data <- checkplate(3)}
+}
+\author{
+ Johannes Ranke
+ \email{jranke@uni-bremen.de}
+ \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{database}
diff --git a/man/checkplate.Rd b/man/checkplate.Rd
deleted file mode 100644
index 794b3f6..0000000
--- a/man/checkplate.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-\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, the databases "cytotox" and "enzymes"
- of the UFT Department of Bioorganic Chemistry are supported (default is
- "cytotox").}
-}
-\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}
-\keyword{internal}

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