#### changes to vignette in light of layout removal Vince Carey authored on 19/06/2012 12:44:32
 ... ... @@ -788,31 +788,31 @@ plot(coex, "neato") 788 788  z <- plot(coex, "neato") 789 789  @ 790 790   791 -The following functions are interfaces to those in BGL, they only calculate  792 -the (x, y)-coordinates of the vertices in the graph. The actual layout is  793 -achieved with additional function, we provide an example on how to do so. 794 - 795 -Following functions are available: 796 - 797 -The \Rfunction{randomGraphLayout} function puts the vertices randomly  798 -on a plane; 799 - 800 -The \Rfunction{circleLayout} function puts the vertices as vertices of  801 -a regular polygon; 802 - 803 -The \Rfunction{kamadaKawaiSpringLayout} function is for connected,  804 -undirected graphs, it treats the edges as springs and tries to minimize  805 -the energy of the whole system; 806 - 807 -The \Rfunction{fruchtermanReingoldForceDirectedLayout} function is for  808 -unweighted, undirected, possibly disconnected graphs, it treats the edges  809 -as forces that pull vertices together, no-edges as forces that push  810 -vertices apart, vertices move to a position as environment changes;  811 -initial positions of the vertices are set randomly by calling  812 -\Rfunction{randomGraphLayout}. Notice that the choice of "width" and  813 -"height" values has dramatic impact on the performance. 814 - 815 -<>= 791 +%The following functions are interfaces to those in BGL, they only calculate  792 +%the (x, y)-coordinates of the vertices in the graph. The actual layout is  793 +%achieved with additional function, we provide an example on how to do so. 794 +% 795 +%Following functions are available: 796 +% 797 +%The \Rfunction{randomGraphLayout} function puts the vertices randomly  798 +%on a plane; 799 +% 800 +%The \Rfunction{circleLayout} function puts the vertices as vertices of  801 +%a regular polygon; 802 +% 803 +%The \Rfunction{kamadaKawaiSpringLayout} function is for connected,  804 +%undirected graphs, it treats the edges as springs and tries to minimize  805 +%the energy of the whole system; 806 +% 807 +%The \Rfunction{fruchtermanReingoldForceDirectedLayout} function is for  808 +%unweighted, undirected, possibly disconnected graphs, it treats the edges  809 +%as forces that pull vertices together, no-edges as forces that push  810 +%vertices apart, vertices move to a position as environment changes;  811 +%initial positions of the vertices are set randomly by calling  812 +%\Rfunction{randomGraphLayout}. Notice that the choice of "width" and  813 +%"height" values has dramatic impact on the performance. 814 + 815 +<>= 816 816  randomGraphLayout(coex) 817 817  circleLayout(coex) 818 818  kamadaKawaiSpringLayout(coex) ... ... @@ -821,10 +821,10 @@ fruchtermanReingoldForceDirectedLayout(coex, 10, 10) 821 821   822 822  Outputs are the (x, y)-coordinates of the vertices in the layout. 823 823   824 -If you want to draw the graphs based on the calculated coordinates, you need  825 -an additional function. The following is an example. 824 +%If you want to draw the graphs based on the calculated coordinates, you need  825 +%an additional function. The following is an example. 826 826   827 -<>= 827 +<>= 828 828  crudeGraphPlot <- function(g, alg=circleLayout, ...) { 829 829  # 830 830  # the alg parameter is a function that computes the ... ... @@ -848,33 +848,33 @@ crudeGraphPlot(coex) 848 848  crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green") 849 849  @ 850 850   851 -<>= 851 +<>= 852 852  crudeGraphPlot(coex) 853 853  @ 854 854   855 -<>= 855 +<>= 856 856  crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green") 857 857  @ 858 858   859 -\begin{figure}[tp] 860 -\begin{center} 861 -\begin{tabular}{cc} 862 -\includegraphics[width=0.49\textwidth]{RBGL-figneato} & 863 -\includegraphics[width=0.49\textwidth]{RBGL-figlayout1} \\ 864 -\includegraphics[width=0.49\textwidth]{RBGL-figlayout2} \\ 865 -\end{tabular} 866 -\end{center} 867 -\caption{\label{fig:graphlayout}% 868 -a) plot(coex, neato). 869 -b) crudeGraphPlot(coex). 870 -c) crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green"). } 871 -\end{figure} 872 - 873 -Call crudeGraphPlot(coex) gives the default circular layout on your graphics device. 874 - 875 -Call crudeGraphPlot(coex, alg=kamada.kawai.spring.layout, col="green") shows you the spring layout with green edges, see Figure~\ref{fig:graphlayout}. 876 - 877 - 859 +%\begin{figure}[tp] 860 +%\begin{center} 861 +%\begin{tabular}{cc} 862 +%\includegraphics[width=0.49\textwidth]{RBGL-figneato} & 863 +%\includegraphics[width=0.49\textwidth]{RBGL-figlayout1} \\ 864 +%\includegraphics[width=0.49\textwidth]{RBGL-figlayout2} \\ 865 +%\end{tabular} 866 +%\end{center} 867 +%\caption{\label{fig:graphlayout}% 868 +%a) plot(coex, neato). 869 +%b) crudeGraphPlot(coex). 870 +%c) crudeGraphPlot(coex, alg=kamadaKawaiSpringLayout, col="green"). } 871 +%\end{figure} 872 +% 873 +%Call crudeGraphPlot(coex) gives the default circular layout on your graphics device. 874 +% 875 +%Call crudeGraphPlot(coex, alg=kamada.kawai.spring.layout, col="green") shows you the spring layout with green edges, see Figure~\ref{fig:graphlayout}. 876 +% 877 +% 878 878  \subsection{Isomorphism} 879 879   880 880  The \Rfunction{isomorphism} function determines if two graphs are isomorphism,