diff options
Diffstat (limited to 'R/drplot.R')
| -rw-r--r-- | R/drplot.R | 36 |
1 files changed, 18 insertions, 18 deletions
@@ -1,12 +1,12 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("dose", "Substance", "mtype")) -drplot <- function(drresults, data, +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", axes = TRUE, frame.plot = TRUE, - postscript = FALSE, pdf = FALSE, png = FALSE, + postscript = FALSE, pdf = FALSE, png = FALSE, bw = TRUE, pointsize = 12, colors = 1:8, ltys = 1:8, pchs = "auto", @@ -24,7 +24,7 @@ drplot <- function(drresults, data, if(is.data.frame(data)) { # Get rid of pseudo substance names of controls nonzerodata <- subset(data,dose!=0) - nonzerodata$substance <- factor(nonzerodata$substance) + nonzerodata$substance <- factor(nonzerodata$substance) zerodata <- subset(data,dose==0) nc <- length(zerodata$dose) # Number of control points if (nc > 0) { @@ -44,12 +44,12 @@ drplot <- function(drresults, data, hr <- max(nonzerodata$response) if (ctype == "std") hr <- max(hr,1 + sdc) if (ctype == "conf") hr <- max(hr,1 + controlconf) - dsubstances <- levels(nonzerodata$substance) + dsubstances <- levels(nonzerodata$substance) } else { lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2 lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2 if (length(subset(drresults,mtype=="linlogit")$Substance) != 0) { - hr <- 1.8 + hr <- 1.8 } else { hr <- 1.0 } @@ -70,20 +70,20 @@ drplot <- function(drresults, data, postscript(file=filename, paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (pdf) { filename = paste(path,fileprefix,".pdf",sep="") pdf(file=filename, paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (png) { filename = paste(path,fileprefix,".png",sep="") png(filename=filename, width=500, height=500, pointsize=pointsize) message("Created File: ",filename,"\n") } - + plot(0,type="n", xlim = xlim, ylim = ylim, @@ -97,7 +97,7 @@ drplot <- function(drresults, data, if (!postscript && !png && !pdf && length(dsubstances) > 1) { op <- par(ask=TRUE) on.exit(par(op)) - } + } } # nl is the overall number of fits to draw by different line types nl <- 0 @@ -123,20 +123,20 @@ drplot <- function(drresults, data, postscript(file=filename, paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (pdf) { filename = paste(path,fileprefix,sub(" ","_",i),".pdf",sep="") pdf(file=filename, paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize) message("Created File: ",filename,"\n") - } + } if (png) { filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="") png(filename=filename, width=500, height=500, pointsize=pointsize) message("Created File: ",filename,"\n") } - + plot(0,type="n", xlim = xlim, ylim = ylim, @@ -147,7 +147,7 @@ drplot <- function(drresults, data, } if (!overlay) legend(lpos, i, lty = 1, col = color, pch = pch, inset=0.05) tmp$dosefactor <- factor(tmp$dose) # necessary because the old - # factor has all levels, not + # factor has all levels, not # only the ones tested with # this substance @@ -157,7 +157,7 @@ drplot <- function(drresults, data, abline(h = 1 + sdc, lty = 2) } if (ctype == "conf") { - abline(h = 1 - controlconf, lty = 2) + abline(h = 1 - controlconf, lty = 2) abline(h = 1 + controlconf, lty = 2) } @@ -179,7 +179,7 @@ drplot <- function(drresults, data, } if (dtype == "conf") { - confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) + confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) tops <- means + confidencedeltas bottoms <- means - confidencedeltas } @@ -207,13 +207,13 @@ drplot <- function(drresults, data, if (drresults[[fit.row, "mtype"]] %in% c("probit", "logit", "weibull", - "linlogit")) + "linlogit")) { m <- attr(drresults, "models")[[as.numeric(fit.row)]] of <- function(x) { predict(m, data.frame(dose = 10^x)) - } - plot(of, lld - 0.5, lhd + 2, + } + plot(of, lld - 0.5, lhd + 2, add = TRUE, col = color, lty = lty) } } |