add a view.legend and a maxerror parameters to the mismatchplot function

R/mismatchplot.R

@@ -26,6 +26,10 @@ NULL
 #' @param inset  the distance to the margin of the legend box (see the \code{\link{legend}} 
 #'               documentation)
 #'               
+#' @param view.legend if set to \code{FALSE} the legend corresponding to the groups is not dispayed.
+#' 
+#' @param maxerror allows for specifying the maximum of errors to display on the graph.
+#' 
 #' @examples
 #' 
 #' # Load the ROBITools library
@@ -48,11 +52,14 @@ NULL
 #' @export
 mismatchplot = function(ecopcr,group=NULL,
                         col=NULL,legend=NULL,
-                        legend.cex=0.7,inset=c(0.02,0.02)) {
+                        legend.cex=0.7,inset=c(0.02,0.02),
+                        view.legend=TRUE,
+                        maxerror=NA) {
   
   maxforward_error = max(ecopcr$forward_mismatch)
   maxreverse_error = max(ecopcr$reverse_mismatch)
-  maxerror=max(maxforward_error,maxreverse_error)
+  if (is.na(maxerror))
+    maxerror=max(maxforward_error,maxreverse_error)
 
   if (is.null(group))
     group=factor(rep("all",dim(ecopcr)[1]))
@@ -65,7 +72,7 @@ mismatchplot = function(ecopcr,group=NULL,
   actualheight= maxerror + 1
   actualwidth = maxerror + 1
   
-  if (length(levels(group)) > 1)
+  if (length(levels(group)) > 1 & view.legend)
     actualwidth = actualwidth + 2
   
   whitepaper(actualwidth,actualheight,xmin=-0.5,ymin=-0.5,asp=1)
@@ -77,8 +84,8 @@ mismatchplot = function(ecopcr,group=NULL,
        labels=0:maxerror)
   
   
-  data = aggregate(group,by=list(forward=ecopcr$forward_mismatch,
-                            reverse=ecopcr$reverse_mismatch),
+  data = aggregate(group,by=list(forward=factor(ecopcr$forward_mismatch,levels=0:maxerror),
+                                 reverse=factor(ecopcr$reverse_mismatch,levels=0:maxerror)),
                    table)
   
   data <- data[rowSums(data[,c(-1,-2),drop=FALSE])>0, , drop=FALSE]
@@ -89,8 +96,8 @@ mismatchplot = function(ecopcr,group=NULL,
   
   
   value=data[,c(-1,-2),drop=FALSE]
-  x = as.integer(data[,1])
-  y = as.integer(data[,2])
+  x = as.integer(data[,1]) - 1
+  y = as.integer(data[,2]) - 1
   diam = sqrt(rowSums(value))
   radius = diam / max(diam) / 2
   
@@ -100,7 +107,7 @@ mismatchplot = function(ecopcr,group=NULL,
                 label="",MoreArgs=list(col=col))
   
   
-  if (length(levels(group)) > 1)
+  if ((length(levels(group))) > 1 & view.legend)
     legend('topright',legend=legend,fill=col, cex=legend.cex, inset=inset)
   
 }