Code:graph plot util
From FinMath
Contents |
[edit] Demonstration
This demonstration will generate a random graph (in the graph theory sense), compute a sensible visual layout based on the topological ordering of nodes, and display it.
fmuse('/graph_plot_util','graphplot.m'); graphplot('demo');
[edit] license.txt
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Library General Public
License version 2 as published by the Free Software Foundation.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
GNU Library General Public License
----------------------------------------------------------------------------
Table of Contents
* GNU LIBRARY GENERAL PUBLIC LICENSE
o Preamble
o TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
----------------------------------------------------------------------------
GNU LIBRARY GENERAL PUBLIC LICENSE
Version 2, June 1991
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[edit] graphplot_readme.txt
Graph visualization (automatic layout) functions ------------------------------------------------ This directory contains code to automatically layout and visualize graphs. It provides a matlab interface to the graphviz program: http://www.research.att.com/sw/tools/graphviz Written by Kevin Murphy, Leon Peshkin, Tom Minka. draw_graph was written by Ali Taylan Cemgil, and is entirely self-contained matlab: it does not need graphviz, but produces lower quality results. http://www.mbfys.kun.nl/~cemgil/matlab/layout.html See also the following URLs for other graph layout programs: http://www.ics.uci.edu/~eppstein/gina/gdraw.html http://www.cwi.nl/InfoVisu/
[edit] depgraph.m
Create a dependency graph for m-files in the current directory. This complements depfun.m and Matlab's dependency report built into the IDE. See also intent.m.
function [A,labels] = depgraph(p) %function [A,labels] = depgraph(p) % % p char (path) % A n x n (dependency graph) % labels n x 1 cell array (node names) % % Create a dependency graph for the current directory % % Peter Cotton, 13-Sep-2007 if nargin<1, p = cd; elseif ~ischar(p) || ~isdir(p), error('depgraph expects a directory as argument'); end w = what(p); nFunc = length(w.m); A = zeros(nFunc); for j=1:nFunc, D = depfun(w.m{j},'-quiet','-toponly'); for k=1:nFunc, if j~=k, fullName = which(w.m{k}); if ismember(fullName,D), A(j,k)=1; end end end end if nargout==0, fmuse('/graph_plot_util','graphplot.m'); notAlone = find(any(A) | any(A')); if isempty(notAlone), title(['No dependencies found in ',p]); else isBox = ones(nFunc,1); % 0 for ellipses, 1 for box graphplot(A(notAlone,notAlone),w.m(notAlone),isBox(notAlone)); title(['Dependency graph for ',p]); end end if nargout==2, labels = w.m; end
[edit] graphplot.m
Plot nodes and edges of a graph using automatic layout generation. This function merely wraps layout and plotting functions written by Kevin Murphy, Leon Peshkin and Tom Minka and is licensed under GNU Library General Public License version 2.
function graphplot(A,varargin) %function graphplot(A,varargin) % % A nNodes x nNodes (adjacency matrix) % % Similar to Mathworks gplot but does not require specification of % coordinates xy. Instead these are autogenerated using code written by % Kevin Murphy, Leon Peshkin and Tom Minka. % % Needs a fix ?! if ischar(A) && strcmpi(A,'demo'), demo_graphplot; else draw_layout(A,varargin{:}); end function demo_graphplot nNodes = 21; edgeDensity = 0.05; A = rand(nNodes)<edgeDensity; graphplot(A); function [x, y, h] = draw_layout(adj, labels, node_t, x, y, varargin) % DRAW_LAYOUT Draws a layout for a graph % % [X, Y, H] = DRAW_LAYOUT(ADJ, <LABELS, ISBOX, X, Y>) % % Inputs : % ADJ : Adjacency matrix (source, sink) % LABELS : Cell array containing labels <Default : '1':'N'> % ISBOX : 1 if node is a box, 0 if oval <Default : zeros> % X, Y, : Coordinates of nodes on the unit square <Default : calls make_layout> % % Outputs : % X, Y : Coordinates of nodes on the unit square % H : Object handles % % Usage Example : [x, y] = draw_layout([0 1;0 0], {'Hidden','Visible'}, [1 0]'); % % h(i,1) is the text handle - color % h(i,2) is the circle handle - facecolor % % See also MAKE_LAYOUT % Change History : % Date Time Prog Note % 13-Apr-2000 9:06 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) % % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl adj = double(adj); N = size(adj,1); if nargin<2, labels = cellstr(int2str((1:N)')); end if nargin<3, node_t = zeros(N,1); else node_t = node_t(:); end; axis([0 1 0 1]); set(gca,'XTick',[],'YTick',[],'box','on'); % axis('square'); %colormap(flipud(gray)); if nargin<4, [x y] = make_layout(adj); end; idx1 = find(node_t==0); h1 = []; wd1=[]; if ~isempty(idx1) [h1 wd1] = textoval(x(idx1), y(idx1), labels(idx1), varargin{:}); end; idx2 = find(node_t~=0); h2 = []; wd2 = []; if ~isempty(idx2) [h2 wd2] = textbox(x(idx2), y(idx2), labels(idx2), varargin{:}); end; wd = zeros(size(wd1,1)+size(wd2,1),2); if ~isempty(idx1), wd(idx1, :) = wd1; end; if ~isempty(idx2), wd(idx2, :) = wd2; end; % bug: this code assumes [x y] is the center of each box and oval, which % isn't exactly true. h_edge = []; for i=1:N, j = find(adj(i,:)==1); for k=j, if x(k)-x(i)==0, sign = 1; if y(i)>y(k), alpha = -pi/2; else alpha = pi/2; end; else alpha = atan((y(k)-y(i))/(x(k)-x(i))); if x(i)<x(k), sign = 1; else sign = -1; end; end; dy1 = sign.*wd(i,2).*sin(alpha); dx1 = sign.*wd(i,1).*cos(alpha); dy2 = sign.*wd(k,2).*sin(alpha); dx2 = sign.*wd(k,1).*cos(alpha); if adj(k,i)==0, % if directed edge h = arrow([x(i)+dx1 y(i)+dy1],[x(k)-dx2 y(k)-dy2],'BaseAngle',30); else h = line([x(i)+dx1 x(k)-dx2],[y(i)+dy1 y(k)-dy2]); adj(k,i)=-1; % Prevent drawing lines twice end; h_edge = [h_edge h]; end; end; color.box = 'black'; color.text = color.box; color.edge = [1 1 1]*3/4; %color.edge = 'green'; if ~isempty(idx1) set(h1(:,1),'Color',color.text) set(h1(:,2),'EdgeColor',color.box) end if ~isempty(idx2) set(h2(:,1),'Color',color.text) set(h2(:,2),'EdgeColor',color.box) end set(h_edge,'Color',color.edge) if nargout>2, h = zeros(length(wd),2); if ~isempty(idx1), h(idx1,:) = h1; end; if ~isempty(idx2), h(idx2,:) = h2; end; end; %%%%% function [t, wd] = textoval(x, y, str, varargin) % TEXTOVAL Draws an oval around text objects % % [T, WIDTH] = TEXTOVAL(X, Y, STR) % [..] = TEXTOVAL(STR) % Interactive % % Inputs : % X, Y : Coordinates % TXT : Strings % % Outputs : % T : Object Handles % WIDTH : x and y Width of ovals % % Usage Example : [t] = textoval('Visit to Asia?'); % % % Note : % See also TEXTBOX % Uses : % Change History : % Date Time Prog Note % 15-Jun-1998 10:36 AM ATC Created under MATLAB 5.1.0.421 % 12-Mar-2004 10:00 AM minka Changed placement/sizing. % % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl temp = []; textProperties = {'BackgroundColor','Color','FontAngle','FontName','FontSize','FontUnits','FontWeight','Rotation'}; varargin = argfilter(varargin,textProperties); if nargin == 1 str = x; end if ~isa(str,'cell') str=cellstr(str); end; N = length(str); wd = zeros(N,2); for i=1:N, if nargin == 1 [x, y] = ginput(1); end tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); % minka [ptc wx wy] = draw_oval(tx); wd(i,:) = [wx wy]; % draw_oval will paint over the text, so need to redraw it delete(tx); tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); temp = [temp; tx ptc]; end if nargout>0, t = temp; end; %%%%%%%%% function [ptc, wx, wy] = draw_oval(tx, x, y) % Draws an oval box around a tex object sz = get(tx,'Extent'); % minka wy = 2/3*sz(4); wx = 2/3*sz(3); x = sz(1)+sz(3)/2; y = sz(2)+sz(4)/2; ptc = ellipse(x, y, wx, wy); set(ptc, 'FaceColor','w'); %%%%%%%%%%%%% function [p] = ellipse(x, y, rx, ry, c) % ELLIPSE Draws Ellipse shaped patch objects % % [<P>] = ELLIPSE(X, Y, Rx, Ry, C) % % Inputs : % X : N x 1 vector of x coordinates % Y : N x 1 vector of y coordinates % Rx, Ry : Radii % C : Color index % % % Outputs : % P = Handles of Ellipse shaped path objects % % Usage Example : [] = ellipse(); % % % Note : % See also % Uses : % Change History : % Date Time Prog Note % 27-May-1998 9:55 AM ATC Created under MATLAB 5.1.0.421 % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl if (nargin < 2) error('Usage Example : e = ellipse([0 1],[0 -1],[1 0.5],[2 0.5]); '); end; if (nargin < 3) rx = 0.1; end; if (nargin < 4) ry = rx; end; if (nargin < 5) c = 1; end; if length(c)==1, c = ones(size(x)).*c; end; if length(rx)==1, rx = ones(size(x)).*rx; end; if length(ry)==1, ry = ones(size(x)).*ry; end; n = length(x); p = zeros(size(x)); t = 0:pi/30:2*pi; for i=1:n, px = rx(i)*cos(t)+x(i); py = ry(i)*sin(t)+y(i); p(i) = patch(px,py,c(i)); end; if nargout>0, pp = p; end; %%%%% function [t, wd] = textbox(x,y,str,varargin) % TEXTBOX Draws A Box around the text % % [T, WIDTH] = TEXTBOX(X, Y, STR) % [..] = TEXTBOX(STR) % % Inputs : % X, Y : Coordinates % TXT : Strings % % Outputs : % T : Object Handles % WIDTH : x and y Width of boxes %% % Usage Example : t = textbox({'Ali','Veli','49','50'}); % % % Note : % See also TEXTOVAL % Uses : % Change History : % Date Time Prog Note % 09-Jun-1998 11:43 AM ATC Created under MATLAB 5.1.0.421 % 12-Mar-2004 10:00 AM minka Changed placement/sizing. % % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl temp = []; textProperties = {'BackgroundColor','Color','FontAngle','FontName','FontSize','FontUnits','FontWeight','Rotation'}; varargin = argfilter(varargin,textProperties); if nargin == 1 str = x; end if ~isa(str,'cell') str=cellstr(str); end; N = length(str); wd = zeros(N,2); for i=1:N, if nargin == 1 [x, y] = ginput(1); end tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); % minka [ptc wx wy] = draw_box(tx); wd(i,:) = [wx wy]; % draw_box will paint over the text, so need to redraw it delete(tx); tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); temp = [temp; tx ptc]; end; if nargout>0, t = temp; end; function [ptc, wx, wy] = draw_box(tx) % Draws a box around a text object sz = get(tx,'Extent'); % minka wy = 1/2*sz(4); wx = 1/2*sz(3); x = sz(1)+sz(3)/2; y = sz(2)+sz(4)/2; ptc = patch([x-wx x+wx x+wx x-wx], [y+wy y+wy y-wy y-wy],'w'); set(ptc, 'FaceColor','w'); function args = argfilter(args,keep) %ARGFILTER Remove unwanted arguments. % ARGFILTER(ARGS,KEEP), where ARGS = {'arg1',value1,'arg2',value2,...}, % returns a new argument list where only the arguments named in KEEP are % retained. KEEP is a character array or cell array of strings. % Written by Tom Minka if ischar(keep) keep = cellstr(keep); end i = 1; while i < length(args) if ~ismember(args{i},keep) args = args(setdiff(1:length(args),[i i+1])); else i = i + 2; end end function [x, y] = make_layout(adj) % MAKE_LAYOUT Creates a layout from an adjacency matrix % % [X, Y] = MAKE_LAYOUT(ADJ) % % Inputs : % ADJ = adjacency matrix (source, sink) % % Outputs : % X, Y : Positions of nodes % % Usage Example : [X, Y] = make_layout(adj); % % % Note : Uses some very simple heuristics, so any other % algorithm would create a nicer layout % % See also % Uses : % Change History : % Date Time Prog Note % 13-Apr-2000 8:25 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl N = size(adj,1); tps = toposort(adj); if ~isempty(tps), % is directed ? level = zeros(1,N); for i=tps, idx = find(adj(:,i)); if ~isempty(idx), l = max(level(idx)); level(i)=l+1; end; end; else level = poset(adj,1)'-1; end; y = (level+1)./(max(level)+2); y = 1-y; x = zeros(size(y)); for i=0:max(level), idx = find(level==i); offset = (rem(i,2)-0.5)/10; x(idx) = (1:length(idx))./(length(idx)+1)+offset; end; %%%%%%% function [depth] = poset(adj, root) % POSET Identify a partial ordering among the nodes of a graph % % [DEPTH] = POSET(ADJ,ROOT) % % Inputs : % ADJ : Adjacency Matrix % ROOT : Node to start with % % Outputs : % DEPTH : Depth of the Node % % Usage Example : [depth] = poset(adj,12); % % % Note : All Nodes must be connected % See also % Uses : % Change History : % Date Time Prog Note % 17-Jun-1998 12:01 PM ATC Created under MATLAB 5.1.0.421 % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl adj = adj+adj'; N = size(adj,1); depth = zeros(N,1); depth(root) = 1; queue = root; while 1, if isempty(queue), if all(depth), break; else root = find(depth==0); root = root(1); depth(root) = 1; queue = root; end; end; r = queue(1); queue(1) = []; idx = find(adj(r,:)); idx2 = find(~depth(idx)); idx = idx(idx2); queue = [queue idx]; depth(idx) = depth(r)+1; end; %%%%%%%%% function [seq] = toposort(adj) % TOPOSORT A Topological ordering of nodes in a directed graph % % [SEQ] = TOPOSORT(ADJ) % % Inputs : % ADJ : Adjacency Matrix. % ADJ(i,j)==1 ==> there exists a directed edge % from i to j % % Outputs : % SEQ : A topological ordered sequence of nodes. % empty matrix if graph contains cycles. % % Usage Example : % N=5; % [l,u] = lu(rand(N)); % adj = ~diag(ones(1,N)) & u>0.5; % seq = toposort(adj); % % % Note : % See also % Uses : % Change History : % Date Time Prog Note % 18-May-1998 4:44 PM ATC Created under MATLAB 5.1.0.421 % ATC = Ali Taylan Cemgil, % SNN - University of Nijmegen, Department of Medical Physics and Biophysics % e-mail : cemgil@mbfys.kun.nl N = size(adj); indeg = sum(adj,1); outdeg = sum(adj,2); seq = []; for i=1:N, % Find nodes with indegree 0 idx = find(indeg==0); % If can't find than graph contains a cycle if isempty(idx), seq = []; break; end; % Remove the node with the max number of connections [dummy idx2] = max(outdeg(idx)); indx = idx(idx2); seq = [seq, indx]; indeg(indx)=-1; idx = find(adj(indx,:)); indeg(idx) = indeg(idx)-1; end; function [h,yy,zz] = arrow(varargin) % ARROW Draw a line with an arrowhead. % % ARROW(Start,Stop) draws a line with an arrow from Start to Stop (points % should be vectors of length 2 or 3, or matrices with 2 or 3 % columns), and returns the graphics handle of the arrow(s). % % ARROW uses the mouse (click-drag) to create an arrow. % % ARROW DEMO & ARROW DEMO2 show 3-D & 2-D demos of the capabilities of ARROW. % % ARROW may be called with a normal argument list or a property-based list. % ARROW(Start,Stop,Length,BaseAngle,TipAngle,Width,Page,CrossDir) is % the full normal argument list, where all but the Start and Stop % points are optional. If you need to specify a later argument (e.g., % Page) but want default values of earlier ones (e.g., TipAngle), % pass an empty matrix for the earlier ones (e.g., TipAngle=[]). % % ARROW('Property1',PropVal1,'Property2',PropVal2,...) creates arrows with the % given properties, using default values for any unspecified or given as % 'default' or NaN. Some properties used for line and patch objects are % used in a modified fashion, others are passed directly to LINE, PATCH, % or SET. For a detailed properties explanation, call ARROW PROPERTIES. % % Start The starting points. B % Stop The end points. /|\ ^ % Length Length of the arrowhead in pixels. /|||\ | % BaseAngle Base angle in degrees (ADE). //|||\\ L| % TipAngle Tip angle in degrees (ABC). ///|||\\\ e| % Width Width of the base in pixels. ////|||\\\\ n| % Page Use hardcopy proportions. /////|D|\\\\\ g| % CrossDir Vector || to arrowhead plane. //// ||| \\\\ t| % NormalDir Vector out of arrowhead plane. /// ||| \\\ h| % Ends Which end has an arrowhead. //<----->|| \\ | % ObjectHandles Vector of handles to update. / base ||| \ V % E angle||<-------->C % ARROW(H,'Prop1',PropVal1,...), where H is a |||tipangle % vector of handles to previously-created arrows ||| % and/or line objects, will update the previously- ||| % created arrows according to the current view -->|A|<-- width % and any specified properties, and will convert % two-point line objects to corresponding arrows. ARROW(H) will update % the arrows if the current view has changed. Root, figure, or axes % handles included in H are replaced by all descendant Arrow objects. % % A property list can follow any specified normal argument list, e.g., % ARROW([1 2 3],[0 0 0],36,'BaseAngle',60) creates an arrow from (1,2,3) to % the origin, with an arrowhead of length 36 pixels and 60-degree base angle. % % The basic arguments or properties can generally be vectorized to create % multiple arrows with the same call. This is done by passing a property % with one row per arrow, or, if all arrows are to have the same property % value, just one row may be specified. % % You may want to execute AXIS(AXIS) before calling ARROW so it doesn't change % the axes on you; ARROW determines the sizes of arrow components BEFORE the % arrow is plotted, so if ARROW changes axis limits, arrows may be malformed. % % This version of ARROW uses features of MATLAB 5 and is incompatible with % earlier MATLAB versions (ARROW for MATLAB 4.2c is available separately); % some problems with perspective plots still exist. % Copyright (c)1995-1997, Erik A. Johnson <johnsone@uiuc.edu>, 8/14/97 % Revision history: % 8/14/97 EAJ Added workaround for MATLAB 5.1 scalar logical transpose bug. % 7/21/97 EAJ Fixed a few misc bugs. % 7/14/97 EAJ Make arrow([],'Prop',...) do nothing (no old handles) % 6/23/97 EAJ MATLAB 5 compatible version, release. % 5/27/97 EAJ Added Line Arrows back in. Corrected a few bugs. % 5/26/97 EAJ Changed missing Start/Stop to mouse-selected arrows. % 5/19/97 EAJ MATLAB 5 compatible version, beta. % 4/13/97 EAJ MATLAB 5 compatible version, alpha. % 1/31/97 EAJ Fixed bug with multiple arrows and unspecified Z coords. % 12/05/96 EAJ Fixed one more bug with log plots and NormalDir specified % 10/24/96 EAJ Fixed bug with log plots and NormalDir specified % 11/13/95 EAJ Corrected handling for 'reverse' axis directions % 10/06/95 EAJ Corrected occasional conflict with SUBPLOT % 4/24/95 EAJ A major rewrite. % Fall 94 EAJ Original code. % Things to be done: % - segment parsing, computing, and plotting into separate subfunctions % - change computing from Xform to Camera paradigms % + this will help especially with 3-D perspective plots % + if the WarpToFill section works right, remove warning code % + when perpsective works properly, remove perspective warning code % - add cell property values and struct property name/values (like get/set) % - get rid of NaN as the "default" data label % + perhaps change userdata to a struct and don't include (or leave % empty) the values specified as default; or use a cell containing % an empty matrix for a default value % - add functionality of GET to retrieve current values of ARROW properties % Many thanks to Keith Rogers <kerog@ai.mit.edu> for his many excellent % suggestions and beta testing. Check out his shareware package MATDRAW. % He has permission to distribute ARROW with MATDRAW. % global variable initialization global ARROW_PERSP_WARN ARROW_STRETCH_WARN ARROW_AXLIMITS if isempty(ARROW_PERSP_WARN ), ARROW_PERSP_WARN =1; end; if isempty(ARROW_STRETCH_WARN), ARROW_STRETCH_WARN=1; end; % Handle callbacks if (nargin>0 & isstr(varargin{1}) & strcmp(lower(varargin{1}),'callback')), arrow_callback(varargin{2:end}); return; end; % Are we doing the demo? c = help/techdoc/ref/sprintf.html">sprintf('\n'); if (help/techdoc/ref/nargin.html">nargin==1 & isstr(help/techdoc/ref/varargin.html">varargin{1})), arg1 = help/techdoc/ref/lower.html">lower(help/techdoc/ref/varargin.html">varargin{1}); if help/techdoc/ref/strncmp.html">strncmp(arg1,'prop',4), arrow_props; elseif help/techdoc/ref/strncmp.html">strncmp(arg1,'demo',4) help/techdoc/ref/clf.html">clf help/techdoc/ref/reset.html">reset demo_info = arrow_demo; if ~