%% BIOGRAPHDEMO Tools for rendering interconnected graph data
% The need for representing interconnected data appears in several
% bioinformatics applications. For example, protein-protein interactions,
% network inference, reaction pathways, cluster data, Bayesian networks,
% and phylogenetic trees can be represented with interconnected graphs. The
% BIOGRAPH object allows you to create a comprehensive and graphical layout
% of this type of data. In this demonstration you learn how to populate a
% BIOGRAPH object, render it, and then modify its properties in order to
% customize its display.

%   Copyright 2003-2004 The MathWorks, Inc.
%   $Revision: 1.1.12.1 $  $Date: 2004/12/24 20:38:14 $

if playbiodemo, return; end % Open in the editor or run step-by-step

%% Representing a phylogenetic tree as a graph
% Read a phylogenetic tree into a PHYTREE object.
tr = phytreeread('pf00002.tree');

%%
% Reduce the tree to only the human proteins (to make the example smaller,
% you can also use the full tree by omitting the following lines).
sel = getbyname(tr,'human');
tr = prune(tr,~sel(1:37))

%%
% The *plot* method for a PHYTREE object can create a basic layout of the
% phylogenetic tree; however, the graph elements are static. 
plot(tr)

%%
% The PHYTREE object information can be put into a BIOGRAPH object, so you
% can create a dynamic layout. First, pull some information from the PHYTREE
% object.
[names,nn,nb,nl] = get(tr,'NodeNames','NumNodes','NumBranches','NumLeaves');
names

%% 
% Notice that the names of the branches are empty. This is fine in a
% PHYTREE object, however, a BIOGRAPH object must have all node IDs unique.
% Give some arbitrary names to the empty IDs.
for k = nl+1:nn
    names{k} = ['Branch ' num2str(k-nl)]; 
end

%%
% You can build a connection matrix up using the *pdist* method for the
% PHYTREE objects. Obtain a pairwise distance matrix by counting tree
% levels between all possible nodes (leaves and branches). We can visualize
% this information with the aid of *imagesc*.

cm = pdist(tr,'criteria','levels','nodes','all','square',true);
figure
imagesc(cm)
colormap(flipud(bone))
axis image
title('Pairwise distances (levels)')

%%
% Pick only the entries which are equal to 1 (which indicate that two nodes
% are directly connected) and entries in the lower triangular part to
% select top-down direct edges.
cm = tril(cm==1);
figure
imagesc(cm)
colormap(flipud(bone))
axis image
title('Top-down direct edges')

%%
% Phylogenetic tree datasets provide the root of the tree as the last
% element in the set. When building a BIOGRAPH connection matrix, it helps
% to reverse the order of both the data and names, so that the graph is
% built from the root out. This will create a more logical and visually
% appealing presentation.
cm = flipud(fliplr(cm));
names = flipud(names);

%%
% Call the BIOGRAPH object constructor with the connection matrix and the
% node IDs. To explore its properties you can use the *get* function.
bg = biograph(cm,names)
get(bg)

%%
% Once a BIOGRAPH object has been created with the essential information
% (the connection matrix and node IDs), you can modify its properties. For
% example, change the layout type to 'radial', which is best for
% phylogenetic data and the scale.

bg.LayoutType = 'radial'; 
bg.LayoutScale = 3/4; 
get(bg)

%%
% Although nodes and edges have been created, the BIOGRAPH object does not
% have the coordinates in which the graph elements should be drawn such
% that its rendering results into a pretty and uncluttered display.
% Before rendering a BIOGRAPH object, you need to calculate an appropriate
% location for every node. *dolayout* is the method that calls the layout
% engine.

%%
% Some properties of the BIOGRAPH object interact with the layout engine,
% among them 'LayoutType' which selects the layout algorithm. 
dolayout(bg)

%%
% Draw the BIOGRAPH object in a viewer window. The method VIEW creates a
% Graphical User Interface (GUI) with the interconnected graph and returns
% a handle to a deep copy of the BIOGRAPH object and which is contained by
% the figure. With this object handle you can later change some of the
% rendering properties.
bgInViewer = view(bg)

%% Changing the BIOGRAPH object properties
% You might want to change the color of all the nodes that represent
% branches. Knowing that the first 'nb' nodes are branches, you can use the 
% vectorized form of *set* to change the 'Color' property of these nodes.
set(bgInViewer.Nodes(1:nb),'Color',[.7 1 .7])

%%
% Changing some properties requires you to run the layout engine again. 
% First change the 'Shape' of the branches to circles.
set(bgInViewer.Nodes(1:nb),'Shape','circle')

%%
% Notice that the new shape is an ellipse and the edges do not connect
% nicely to the limits of new shapes.

%%
% Now, run the layout engine over the BIOGRAPH object contained by the
% viewer to correct the shapes and the edges.
dolayout(bgInViewer)

%%
% The extent (size) of the nodes is estimated automatically using the
% node 'FontSize' and 'Label' properties. You can force the nodes to have
% any size by turning off the BIOGRAPH 'NodeAutoSize' property and then
% refreshing the layout.
bgInViewer.NodeAutoSize = 'off';
set(bgInViewer.Nodes(1:nb),'Size',[20 20])
set(bgInViewer.Nodes(1:nb),'Label','')
dolayout(bgInViewer)