## 
# mae.ColorBasedMatrixPlotting() - plot to generate coding for groups with color.
# Parameters:
#   uniqGroups - Vector of unique groups
#   group  - Matrix of the group for the rows of x
#   data   - The data matrix
# Shyam(shyamss@hotmail.com)
# Date : 07/18/2002
##
mae.colorBasedMatrixPlotting <- function(uniqGroups ,group, data, xindex=1,
                                         yindex=2, gbgcolor="black",
                                         xlabel="PC1", ylabel="PC2", mainTitle,
                                         xrange=range(data),yrange=range(data))
{ # mae.colorBasedMatrixPlotting
  uniqGroups <- as.matrix(uniqGroups )
  group <- as.matrix(group)
  data <- as.matrix(data)

  loop <- 1
  fgcolor <-"black"
  if(gbgcolor == "white") 
    colors <- cbind("yellow","red","blue","green","magenta","pink",
                    "cyan","black")
  else
    colors <- cbind("yellow","red","blue","green","magenta","pink",
                    "cyan","white")

 clr <- 0
 for( x in uniqGroups )
 { # x_loop
   clr <- clr+1
   if (clr > 8)
    clr <- 1
   boolX <- as.matrix(group[,1]==x)
   pts <- matrix(data[boolX,], nc=ncol(data))
   colors[clr]
   if (loop==1)
   { # main plot 1st time through the loop
     plot(xrange,yrange,col="transparent",xlim=xrange,ylim=yrange,xlab=xlabel,
          ylab=ylabel,main=mainTitle,pch=20,col.lab=fgcolor,col.axis=fgcolor,
          col.main=fgcolor)
     if (gbgcolor == "black")
     {
       rect(xrange[1]-(.039*(xrange[2]-xrange[1])),
            yrange[1]-(.039*(yrange[2]-yrange[1])),
            xrange[2]+(.039*(xrange[2]-xrange[1])), 
            yrange[2]+(.039*(yrange[2]-yrange[1])),
            col=gbgcolor, border=gbgcolor)
     }
   }
   points(pts[,xindex],pts[,yindex], col=colors[clr],pch=20 )
   loop <- loop + 1            # next group
  } # x_loop
} # end of mae.colorBasedMatrixPlotting