Comparative_MEA_dataset/Codes/Connectivity Analysis/map.m

%% for one way connections comment out if not used
source_1=source;
target_1=target;
for i=1:length(source)
    temp=[source(i) target_1(i)];
    in1=find(target==temp(1,1));
    in2=find(source==temp(1,2));
    if isempty(intersect(in1,in2))~= 1
        source(i)=0;
        target(i)=0;
        weight(i)=0;
    end
end
source=(nonzeros(source))';
target=(nonzeros(target))';
weight=(nonzeros(weight))';
%%

clear channels
clear ids
j=1;
channels(j)=source(1);
for i=2:length(source)      %finds all source channels and add them to channels
    if source(i)~=channels
        j=j+1;
        channels(j)=source(i);
    end
end

for i=1:length(target)
    if target(i)~=channels
        j=j+1;
        channels(j)=target(i); %finds also all target channels and add them
    end                       %to channels if they are not added as source before
end

N=length(channels);
cm=zeros(N,N);
weight_new=zeros(N,N);


for i=1:length(channels)
    [row,col]=find(source==channels(i)) %make connections from source to target
    if size(row) ~= 0
        x=target(row,col);
        x=x(1,:);
        for j=1: length(row)
            [row1,col1]=find(channels==x(j))
            cm(i,col1)=1;
            weight_new (i,col1) = cross(channels(i),channels(col1));%%THIS PART IS ADDED AFTER REALIZING THE MISTAKE IN PUBLICATION...REORDERS THE WEIGHTS OF LINKS RIGHT WAY
        end
    end
   
end




for k=1:N
    ChannelName{k} = DataCell{channels(k),1}(end-3:end);
    ids{k}=['' ChannelName{k} ''''];
end



%%
bg2=biograph(cm,ids,'NodeAutoSize','off','ShowArrows','off');

    get(bg2.nodes,'ID')
    set(bg2, 'EdgeType', 'curved')
    hbg= view(bg2);



%% DO LAYOUT ACCORDING TO MEA SETUP
page_Size = [400 400];

XpageSize = page_Size(1);
YpageSize = page_Size(2);

for i = 1:length(ids)
nodeID = str2num(ids{i}(end-2:end-1));
tens = floor(nodeID / 10);
ones = mod(nodeID , 10);
xposition = floor(XpageSize / 8) * tens ;
yposition = floor(YpageSize / 8) * (ones); %(9-ones) for MCS setup; (ones) for Axion setup
set(hbg.Nodes(i),'Position', [xposition, yposition]);
set(hbg.Nodes(i),'Color', [51/255 204/255 204/255]);%[20/255 108/255 217/255]);%[196/255 4/255 33/255]);%[51/255 204/255 204/255]);%[230/255 160/255 45/255]);%
set(hbg.Nodes(i),'LineColor', [51/255 204/255 204/255]);%[196/255 4/255 33/255]);%[51/255 204/255 204/255]);%[230/255 160/255 45/255]);
set(hbg.Nodes(i),'FontSize', 12);%12); in original 12
set(hbg.Nodes(i),'Shape', 'circle');
set(hbg.Nodes(i),'Size', [30 30]);% [30 30]); in original 30
end
%% SET PATH WIDTHS ACCORDING TO CORRELATION COEFFICIENTS i.e WEIGHTS
% Set the weights in the right order reading as it is in cm
weight_row=[]; 
weight_col=[];
for t = 1 : length(weight_new)
    [a, b]=find(weight_new(t,:)~=0);
   if size(b) ~= 0  
       weight_row=[weight_row (a*t)];
       weight_col=[weight_col b];
   end
end
% added the correct till here

for i = 1:length(weight_row)
set(hbg.Edges(i),'LineWidth', (10*(abs(weight_new(weight_row(i),weight_col(i)))-treshold)+0.1)); % default (10*(abs(weight_new(weight_row(i),weight_col(i)))-treshold)+0.1 ))
end
%%
set(hbg.Edges,'LineColor', [0/255 0/255 0/255]);
dolayout(hbg, 'Pathsonly', true)