From c5315525c80a6822eef2311e6b0733ee5018db60 Mon Sep 17 00:00:00 2001
From: ranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>
Date: Mon, 3 Apr 2006 16:28:19 +0000
Subject: - The drplot function now accepts custom xlim and ylim values -
 Confidence intervals for the EC50 can now (again) be generated by   drfit by
 giving the argument conf=TRUE - Update of the INDEX

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@62 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
---
 R/drplot.R | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

(limited to 'R/drplot.R')

diff --git a/R/drplot.R b/R/drplot.R
index baec69d..8faaa0f 100644
--- a/R/drplot.R
+++ b/R/drplot.R
@@ -1,6 +1,7 @@
 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,
@@ -14,14 +15,15 @@ drplot <- function(drresults, data,
         unit <- "different units"
     }
 
-    # Get the plot limits on the x-axis (log of the dose) and y axis
+    # 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) # Get rid of pseudo substance names of controls
+        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)    # Standard deviation of control responses
+            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")
@@ -52,6 +54,12 @@ drplot <- function(drresults, data,
             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)
@@ -79,10 +87,10 @@ drplot <- function(drresults, data,
         }
             
         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")
+            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
@@ -123,10 +131,10 @@ drplot <- function(drresults, data,
                     }
                         
                     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")
+                        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
-- 
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