diff options
Diffstat (limited to 'R/drplot.R')
| -rw-r--r-- | R/drplot.R | 36 |
1 files changed, 22 insertions, 14 deletions
@@ -2,10 +2,12 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95, ctype = "none", path = "./", fileprefix = "drplot", overlay = FALSE, xlim = c("auto","auto"), ylim = c("auto","auto"), + xlab = paste("Decadic Logarithm of the dose in ", unit), + ylab = "Normalized response", postscript = FALSE, pdf = FALSE, png = FALSE, bw = TRUE, pointsize = 12, - colors = 1:8, devoff=T, lpos="topright") + colors = 1:8, ltys = 1:8, devoff=T, lpos="topright") { # Check if all data have the same unit unitlevels <- levels(as.factor(drresults$unit)) @@ -81,8 +83,8 @@ drplot <- function(drresults, data, plot(0,type="n", xlim = xlim, ylim = ylim, - xlab = paste("Decadic Logarithm of the dose in ", unit), - ylab = "Normalized response") + xlab = xlab, + ylab = ylab) } else { # If overlay plot is not requested, ask before showing multiple plots on the screen if (!postscript && !png && !pdf && length(dsubstances) > 1) { @@ -90,6 +92,8 @@ drplot <- function(drresults, data, on.exit(par(op)) } } + # nl is the overall number of fits to draw by different line types + nl <- 0 # Plot the data either as raw data or as error bars if(is.data.frame(data)) { @@ -97,7 +101,7 @@ drplot <- function(drresults, data, # n is the index for the dose-response curves n <- 0 if (bw) colors <- rep("black",length(dsubstances)) - # Loop over the substances in the data + # Loop over the substances in the data (index n) for (i in dsubstances) { n <- n + 1 tmp <- splitted[[i]] @@ -128,10 +132,10 @@ drplot <- function(drresults, data, plot(0,type="n", xlim = xlim, ylim = ylim, - xlab = paste("Decadic Logarithm of the dose in ", unit), - ylab = "Normalized response") + xlab = xlab, + ylab = ylab) } - if (!overlay) legend(lpos, i,lty = 1, col = color, inset=0.05) + if (!overlay) legend(lpos, i, lty = 1, col = color, inset=0.05) tmp$dosefactor <- factor(tmp$dose) # necessary because the old # factor has all levels, not # only the ones tested with @@ -180,31 +184,35 @@ drplot <- function(drresults, data, } } - # Plot the fits, if there are any + # Plot the fits for this substance, if there are any fits <- subset(drresults,Substance == i) - nf <- length(fits$Substance) # number of fits to plot + nf <- length(fits$Substance) # number of fits to plot for this substance if (nf > 0) { for (j in 1:nf) { logED50 <- fits[j,"logED50"] mtype <- as.character(fits[j, "mtype"]) if (mtype == "probit") { + lty <- ltys[nl <- nl + 1] scale <- fits[j,"b"] - plot(function(x) pnorm(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color) + plot(function(x) pnorm(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE, col=color, lty=lty) } if (mtype == "logit") { + lty <- ltys[nl <- nl + 1] scale <- fits[j,"b"] - plot(function(x) plogis(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE,col=color) + plot(function(x) plogis(-x,-logED50,scale),lld - 0.5, lhd + 2, add=TRUE, col=color, lty=lty) } if (mtype == "weibull") { + lty <- ltys[nl <- nl + 1] location <- fits[j,"a"] shape <- fits[j,"b"] - plot(function(x) pweibull(-x+location,shape),lld - 0.5, lhd + 2, add=TRUE,col=color) + plot(function(x) pweibull(-x+location,shape),lld - 0.5, lhd + 2, add=TRUE, col=color, lty=lty) } if (mtype == "linlogit") { + lty <- ltys[nl <- nl + 1] 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) + add=TRUE, col=color, lty=lty) } } } @@ -214,7 +222,7 @@ drplot <- function(drresults, data, } } } - if (overlay) legend(lpos, dsubstances,lty = 1, col = colors, inset=0.05) + if (overlay) legend(lpos, dsubstances, col = colors, lty = ltys, inset=0.05) if (overlay && (postscript || png || pdf)) { if (devoff) { dev.off() |