From 6d0fa52837e7f2220846203b07e2dbc3d6846253 Mon Sep 17 00:00:00 2001 From: ranke Date: Mon, 14 Mar 2005 07:42:30 +0000 Subject: 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 --- DESCRIPTION | 4 +- R/drfit.R | 1051 +++++++++++++++++++++++++------------------------ man/checksubstance.Rd | 6 +- man/drplot.Rd | 4 +- 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 Maintainer: Johannes Ranke 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 -- cgit v1.2.1