diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/drfit.R | 46 |
1 files changed, 36 insertions, 10 deletions
@@ -287,7 +287,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE, return(results) } -drplot <- function(drresults, data, dtype = "std", alpha = 0.95, +drplot <- function(drresults, data, + dtype = "std", alpha = 0.95, ctype = "none", path = "./", fileprefix = "drplot", overlay = FALSE, postscript = FALSE, png = FALSE, bw = TRUE, pointsize = 12, @@ -301,16 +302,30 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95, unit <- "different units" } - # Get the plot limits on the x-axis (log of the dose) + # Get the plot limits on the x-axis (log of the dose) and y axis 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)) + nonzerodata <- subset(data,dose!=0) + nonzerodata$substance <- factor(nonzerodata$substance) # Get rid of pseudo substance names of controls + zerodata <- subset(data,dose==0) + nc <- length(zerodata$dose) # Number of control points + sdc <- sd(zerodata$response) # Standard deviation of control responses + controlconf <- sdc * qt((1 + alpha)/2, nc - 1) / sqrt(nc) + if (nc > 0) { + 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" + } } - lhd <- log10(max(data$dose)) - hr <- max(data$response) - dsubstances <- levels(data$substance) + lld <- log10(min(nonzerodata$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$substance) } else { lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2 lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2 @@ -349,7 +364,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95, # Plot the data either as raw data or as error bars if(is.data.frame(data)) { - splitted <- split(data,data$substance) + splitted <- split(nonzerodata,nonzerodata$substance) # n is the index for the dose-response curves n <- 0 if (bw) colors <- rep("black",length(dsubstances)) @@ -389,6 +404,17 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95, # 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") { |