draw_brainNetworks.m

function ax = draw_brainNetworks(ax, connectome, node_interest, nodeLocations, ...
                                 threshold, markersize, node_interest_data, node_interest_cmap, ...
                                 node_interest_markersize, edge_color, slice)
% draw_brainNetworks.m
%
% Draw a scatter plot of brain nodes and top connections per node_interest
% in a particular view slice
%
% Inputs: ax                       : axis handle to plot on
%         connectome               : weighted connectivity matrix [NxN]
%         node_interest            : nodes to highlight [1xM]
%         nodeLocations            : 3D locations of the nodes [Nx3]
%         threshold                : threshold of weights to show in % (float)
%         markersize               : uniform size of the nodes (float)
%         node_interest_data       : properties of node_interest [1xM]
%         node_interest_cmap       : colormap of node_interest_data [Mx3]
%         node_interest_markersize : markersize of node_interest [float]
%         edge_color               : color of edges (string) or [1x3]
%         slice                    : view slice (string)
%                                    'axial', 'sagittal_left', 'sagittal_right',
%                                    'coronal'
% Outputs: ax                      : redefine initial axis handle
%
% Original: James Pang, QIMR Berghofer, 2020

%%
if strcmpi(slice, 'axial')
    nodeLocations = cat(2, nodeLocations(:,1), nodeLocations(:,2), nodeLocations(:,3));
elseif strcmpi(slice, 'sagittal_left')
    nodeLocations = cat(2, -nodeLocations(:,2), nodeLocations(:,3), -nodeLocations(:,1));
elseif strcmpi(slice, 'sagittal_right')
    nodeLocations = cat(2, nodeLocations(:,2), nodeLocations(:,3), nodeLocations(:,1));
elseif strcmpi(slice, 'coronal')
    nodeLocations = cat(2, nodeLocations(:,1), nodeLocations(:,3), -nodeLocations(:,2));
end

N = size(connectome,2);
noninterest = setdiff(1:N, node_interest);

scatterBrain_all(ax, nodeLocations(noninterest,:), markersize);
hold on;
scatter3(ax, nodeLocations(node_interest,1), nodeLocations(node_interest,2), nodeLocations(node_interest,3), ...
                   node_interest_markersize, node_interest_data, 'filled', 'markeredgecolor', 'k');

for node_ind = 1:length(node_interest)
    node = node_interest(node_ind);
    weights = connectome(node,:);
    [~, sort_ind] = sort(weights, 'descend');
    num_connections = floor((threshold/100)*length(weights));
    top_connections_nodes = sort_ind(1:num_connections);

    if num_connections>0
        for connection = 1:num_connections
            line(ax, 'XData',nodeLocations([node,top_connections_nodes(connection)],1), ...
                     'YData',nodeLocations([node,top_connections_nodes(connection)],2), ...
                     'ZData',nodeLocations([node,top_connections_nodes(connection)],3), ...
                     'linewidth', 0.5, 'color', edge_color)
        end
    end
end
hold off;
set(ax, 'colormap', node_interest_cmap)
view(ax, 2)
axis(ax, 'equal')
set(ax, 'visible', 'off')

end

function obj = scatterBrain_all(ax, nodeLocations, markersize)

obj = scatter3(ax, nodeLocations(:,1), nodeLocations(:,2), nodeLocations(:,3), ...
                markersize, 'markeredgecolor', 0.3*[1 1 1], 'markerfacecolor', 'none', ...
                'markeredgealpha', 0.3);
            
end