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drplot <- function(drresults, data,
dtype = "std", alpha = 0.95, ctype = "none",
path = "./", fileprefix = "drplot", overlay = FALSE,
xlim = c("auto","auto"), ylim = c("auto","auto"),
postscript = FALSE, pdf = FALSE, png = FALSE,
bw = TRUE,
pointsize = 12,
colors = 1:8, devoff=T, lpos="topright")
{
# Check if all data have the same unit
unitlevels <- levels(as.factor(drresults$unit))
if (length(unitlevels) == 1) {
unit <- unitlevels
} else {
unit <- "different units"
}
# Determine the plot limits on the x-axis and y axis
if(is.data.frame(data)) {
# Get rid of pseudo substance names of controls
nonzerodata <- subset(data,dose!=0)
nonzerodata$substance <- factor(nonzerodata$substance)
zerodata <- subset(data,dose==0)
nc <- length(zerodata$dose) # Number of control points
if (nc > 0) {
sdc <- sd(zerodata$response)
controlconf <- sdc * qt((1 + alpha)/2, nc - 1) / sqrt(nc)
cat("There are ",nc,"data points with dose 0 (control values)\n")
cat("with a standard deviation of",sdc,"\n")
cat("and a confidence interval of",controlconf,"\n")
if (nc < 3) {
cat("\nThere are less than 3 control points, therefore their scatter\n")
cat("will not be displayed\n")
ctype = "none"
}
} else {
if (ctype != "none") {
stop("There are no controls in the dataset, and therefore ",
"their scatter cannot be displayed\n")
}
}
lld <- log10(min(nonzerodata$dose))
lhd <- log10(max(nonzerodata$dose))
hr <- max(nonzerodata$response)
if (ctype == "std") hr <- max(hr,1 + sdc)
if (ctype == "conf") hr <- max(hr,1 + controlconf)
dsubstances <- levels(nonzerodata$substance)
} else {
lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2
lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2
if (length(subset(drresults,mtype=="linlogit")$Substance) != 0) {
hr <- 1.8
} else {
hr <- 1.0
}
}
if (xlim[1] == "auto") xlim[1] <- lld - 0.5
if (xlim[2] == "auto") xlim[2] <- lhd + 1
if (ylim[1] == "auto") ylim[1] <- -0.1
if (ylim[2] == "auto") ylim[2] <- hr + 0.2
xlim <- as.numeric(xlim)
ylim <- as.numeric(ylim)
# 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=pointsize)
cat("Created File: ",filename,"\n")
}
if (pdf) {
filename = paste(path,fileprefix,".pdf",sep="")
pdf(file=filename,
paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
cat("Created File: ",filename,"\n")
}
if (png) {
filename = paste(path,fileprefix,".png",sep="")
png(filename=filename,
width=500, height=500, pointsize=pointsize)
cat("Created File: ",filename,"\n")
}
if (!postscript && !png && !pdf) {
get(getOption("device"))(width=7,height=7)
}
plot(0,type="n",
xlim = xlim,
ylim = ylim,
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(nonzerodata,nonzerodata$substance)
# n is the index for the dose-response curves
n <- 0
if (bw) colors <- rep("black",length(dsubstances))
# Loop over the substances in the data
for (i in dsubstances) {
n <- n + 1
tmp <- splitted[[i]]
if (length(tmp$response) != 0) {
color <- colors[[n]]
# Prepare the single graphs if an overlay is not requested
if (!overlay)
{
if (postscript) {
filename = paste(path,fileprefix,sub(" ","_",i),".eps",sep="")
postscript(file=filename,
paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
cat("Created File: ",filename,"\n")
}
if (pdf) {
filename = paste(path,fileprefix,sub(" ","_",i),".pdf",sep="")
pdf(file=filename,
paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
cat("Created File: ",filename,"\n")
}
if (png) {
filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="")
png(filename=filename,
width=500, height=500, pointsize=pointsize)
cat("Created File: ",filename,"\n")
}
if (!postscript && !png && !pdf) {
get(getOption("device"))(width=7,height=7)
}
plot(0,type="n",
xlim = xlim,
ylim = ylim,
xlab = paste("Decadic Logarithm of the dose in ", unit),
ylab = "Normalized response")
}
if (!overlay) legend(lpos, i,lty = 1, col = color, inset=0.05)
tmp$dosefactor <- factor(tmp$dose) # necessary because the old
# factor has all levels, not
# only the ones tested with
# this substance
# Plot the control lines, if requested
if (ctype == "std") {
abline(h = 1 - sdc, lty = 2)
abline(h = 1 + sdc, lty = 2)
}
if (ctype == "conf") {
abline(h = 1 - controlconf, lty = 2)
abline(h = 1 + controlconf, lty = 2)
}
# 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)
{
logED50 <- fits[j,"logED50"]
mtype <- as.character(fits[j, "mtype"])
if (mtype == "probit") {
scale <- fits[j,"b"]
plot(function(x) pnorm(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color)
}
if (mtype == "logit") {
scale <- fits[j,"b"]
plot(function(x) plogis(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color)
}
if (mtype == "weibull") {
location <- fits[j,"a"]
shape <- fits[j,"b"]
plot(function(x) pweibull(-x+location,shape),lld - 0.5, lhd + 2, add=TRUE,col=color)
}
if (mtype == "linlogit") {
plot(function(x) linlogitf(10^x,1,fits[j,"c"],fits[j,"logED50"],fits[j,"b"]),
lld - 0.5, lhd + 2,
add=TRUE,col=color)
}
}
}
if (!overlay && (postscript || png || pdf)) dev.off()
} else {
cat("No data for ",i,"\n")
}
}
}
if (overlay) legend(lpos, dsubstances,lty = 1, col = colors, inset=0.05)
if (overlay && (postscript || png || pdf)) {
if (devoff) {
dev.off()
}
}
}
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