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Slepi/Code/PlotBrainGraph.m
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PlotBrainGraph.m
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%% This function uses routines formerly implemented in MIP:Lab (Jonas
% Richiardi) to plot brain plots
%
% Inputs:
% - CM is a n_ROI x n_ROI matrix denoting the strength of connections (if
% wished in the plot). One can enter a matrix full of zeros if connections
% should not be displaye
% - CC is a vector representing the size of the nodes in the plot
% - CodeBook contains the information about where to locate the nodes of
% the atlas, and how to label them
% - T_conn is the treshold above which connections will be represented. For
% example, if we have a FC matrix and T_conn=0.5, only the strongest
% positive connections will be displayed
% - Factor_SphereSize rescales the size of the nodes; recommanded value is
% the max of the CC vector or something similar
% - Same for Factor_Col, but controling the color of the nodes
% - Exp_Sphere controls the linearity of the sphere sizes (quadratically
% increasing in the display if Exp_Sphere=2)
% - View is an integer from 1 to 3 depicting the type of slices to show
% - Colormap_nodes is the matlab colormap to use to represent nodes (e.g.
% 'hot' or 'autumn'
% - Colormap_edges is the matlab colormap to use to represent edges
% - Gamma is a factor controling the linear of edge thickness when plotting
% connections
% - LinearWeight is a rescaling factor for connections
% - CA can be set to [] to have dynamic ranges for the connection colormap;
% if set to something specific, that range is used for the plotting
function [] = PlotBrainGraph(CM,CC,CC2,CodeBook,T_conn,Factor_SphereSize,...
Factor_Col,Exp_Sphere,View,Colormap_nodes,Colormap_edges,Gamma,...
LinearWeight,CA)
% edges
pp.doPlotConnections=1;
pp.pruneTinyConnections=1;
pp.pruningWeight=T_conn;
pp.linearWeight=LinearWeight;
pp.gamma=Gamma;
pp.doColourCode=true;
pp.cmapchoiceE=Colormap_edges;
% nodes
pp.doPlotDegreeSpheres=true;%**
pp.myDSplotT=0; % this * 1/N is the threshold
pp.showLabels=0;
pp.cmapchoiceV=Colormap_nodes; % gray
% Controls the exponent for the display of the spheres
pp.e_matD_to_sphS=Exp_Sphere;
pp.f_matD_to_sphS=1;
% brain outline
pp.bmesh_faceAlpha=0.2; % transparency
% node size and color
pp.FctForColSph=CC2/Factor_Col;
pp.FctForSizSph=CC/Factor_SphereSize;
% Edge transparency
pp.doAlpha = true;
pp.alphagamma = 0.05;
figure
if ~isempty(CA)
[~]=show_cm_extended(CM,CC,CC2,CodeBook.full,3,'gamma',pp.gamma,'FctForColSph',pp.FctForColSph,...
'linearWeight',pp.linearWeight,'showLabels',pp.showLabels,...
'createFigure',false,'doColourCode',pp.doColourCode,'doAlpha',pp.doAlpha,'alphagamma',pp.alphagamma,...
'cmapchoiceV',pp.cmapchoiceV,'cmapchoiceE',pp.cmapchoiceE,...
'doPlotConnections',pp.doPlotConnections,'doPlotDegreeSpheres',pp.doPlotDegreeSpheres,...
'bmesh_show',1,'bmesh_hemi','lr','bmesh_useConvexHull',false,...
'bmesh_convexHullOutlinePlanes','','FctForSizSph',pp.FctForSizSph,...
'bmesh_faceAlpha',pp.bmesh_faceAlpha,'pruneTinyConnections',pp.pruneTinyConnections,...
'pruningWeight',pp.pruningWeight,'e_matD_to_sphS',pp.e_matD_to_sphS,'f_matD_to_sphS', pp.f_matD_to_sphS,...
'plotDegreeSpheresOnlyAboveThreshold',pp.myDSplotT,...
'showTopNlabels',0,'txtPosOffset',5*[1 1 1],'ColAxis',CA,...
'showTopNlabelsBy','vertexW','useShortNames',0);
else
[~]=show_cm_extended(CM,CC,CC2,CodeBook.full,3,'gamma',pp.gamma,'FctForColSph',pp.FctForColSph,...
'linearWeight',pp.linearWeight,'showLabels',pp.showLabels,...
'createFigure',false,'doColourCode',pp.doColourCode,'doAlpha',pp.doAlpha,'alphagamma',pp.alphagamma,...
'cmapchoiceV',pp.cmapchoiceV,'cmapchoiceE',pp.cmapchoiceE,...
'doPlotConnections',pp.doPlotConnections,'doPlotDegreeSpheres',pp.doPlotDegreeSpheres,...
'bmesh_show',1,'bmesh_hemi','lr','bmesh_useConvexHull',false,...
'bmesh_convexHullOutlinePlanes','','FctForSizSph',pp.FctForSizSph,...
'bmesh_faceAlpha',pp.bmesh_faceAlpha,'pruneTinyConnections',pp.pruneTinyConnections,...
'pruningWeight',pp.pruningWeight,'e_matD_to_sphS',pp.e_matD_to_sphS,'f_matD_to_sphS', pp.f_matD_to_sphS,...
'plotDegreeSpheresOnlyAboveThreshold',pp.myDSplotT,...
'showTopNlabels',0,'txtPosOffset',5*[1 1 1],...
'showTopNlabelsBy','vertexW','useShortNames',0);
end
%colorbar;
axis off
axis tight;
if View==1, az=0; el=90; cam='right'; vview='ax';
elseif View==2, az=90; el=0; cam='right'; vview='sag';
else az=0; el=0; cam='left'; vview='cor';
end
view(az,el);
camlight(cam);
disp('done');
end
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