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[NET-314] Scaling and color choice on chord plots #160

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431eafe
added scaling and colormap choice to chords
pollaro Jul 2, 2026
6226dca
hopefully centering plots together
pollaro Jul 6, 2026
3121116
Exported mlapp files
actions-user Jul 6, 2026
4f9410c
edge chord scaling
pollaro Jul 6, 2026
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187 changes: 167 additions & 20 deletions +nla/+net/+result/+chord/ChordPlotter.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,16 @@
axis_width = 750; % Constant for the size of the chord
trimatrix_width = 500; % Constant for the size of the Trimatrix plotted with
bottom_text_height = 250; % How far from the bottom of the trimatrix the text appears
colormap_choices = {"Parula", "Turbo", "HSV", "Hot", "Cool", "Spring", "Summer", "Autumn", "Winter", "Gray",...
"Bone", "Copper", "Pink"}; % Colorbar choices
end

properties
network_atlas % Network Atlas for the data
edge_test_result % Edge test results
split_plot = false % This is an option that is set automatically during operation.
edge_plot_type = "nla.gfx.EdgeChordPlotMethod.PROB" % Default chord type for edges
chord_plotter = false
end

methods
Expand All @@ -30,11 +33,14 @@
end
end

function generateChordFigure(obj, parameters, chord_type)
function generateChordFigure(obj, parameters, chord_type, parent_figure)
% generateChordFigure plots chords for a network test
import nla.gfx.SigType nla.net.result.plot.PermutationTestPlotter nla.gfx.EdgeChordPlotMethod nla.gfx.setTitle

coefficient_bounds = [0, parameters.p_value_plot_max];
if isfield(parameters, "lower_bound")
coefficient_bounds(1) = parameters.lower_bound;
end
if parameters.significance_type == SigType.INCREASING && parameters.p_value_plot_max < 1
coefficient_bounds = [parameters.p_value_plot_max, 1];
end
Expand All @@ -53,6 +59,9 @@ function generateChordFigure(obj, parameters, chord_type)
else
plot_figure = nla.gfx.createFigure(obj.axis_width , obj.axis_width);
end
if ~isequal(parent_figure, false)
nla.gfx.moveFigToParentUILocation(plot_figure, parent_figure);
end

% Plot a standard chord plot
if chord_type == "nla.PlotType.CHORD"
Expand All @@ -68,26 +77,38 @@ function generateChordFigure(obj, parameters, chord_type)
% thresholding below the "insignificance" value
statistic_matrix = copy(parameters.statistic_plot_matrix);
statistic_matrix.v(~parameters.significance_plot.v) = insignificance;
chord_plotter = nla.gfx.chord.ChordPlot(obj.network_atlas, figure_axis, 500, statistic_matrix,...
obj.chord_plotter = nla.gfx.chord.ChordPlot(obj.network_atlas, figure_axis, 500, statistic_matrix,...
'color_map', parameters.color_map, 'direction', parameters.significance_type, 'upper_limit',...
coefficient_bounds(2), 'lower_limit', coefficient_bounds(1), 'chord_type', chord_type);
chord_plotter.drawChords();
obj.chord_plotter.drawChords();
setTitle(figure_axis, parameters.name_label)
settings_menu = uimenu(plot_figure, 'Text', 'Settings');
change_scale_option = uimenu(settings_menu,'Text','Change Scale');
change_scale_option.MenuSelectedFcn = {@obj.adjustScale, coefficient_bounds, plot_figure, parameters, chord_type};
change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
change_color_map.MenuSelectedFcn = {@obj.adjustColor, plot_figure, parameters, chord_type};
else
% Plot edge chord
obj.generateEdgeChordFigure(plot_figure, parameters, chord_type)
obj.generateEdgeChordFigure(plot_figure, parameters, chord_type, parent_figure)
end


end
end

methods (Access = protected)
function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type)
function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type, parent_figure)
% generateEdgeChordFigure generates the edge chord plotting
import nla.gfx.EdgeChordPlotMethod nla.gfx.setTitle

range_limit = std(obj.edge_test_result.coeff.v) * 5;
coefficient_min = -range_limit;
coefficient_max = range_limit;
if isfield(parameters, "lower_bound")
coefficient_min = parameters.lower_bound;
coefficient_max = parameters.p_value_plot_max;
else
range_limit = std(obj.edge_test_result.coeff.v) * 5;
coefficient_min = -range_limit;
coefficient_max = range_limit;
end

clipped_values = nla.TriMatrix(obj.network_atlas.numROIs(), nla.TriMatrixDiag.REMOVE_DIAGONAL);
clipped_values.v = obj.edge_test_result.coeff.v;
Expand All @@ -110,21 +131,39 @@ function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type)
switch obj.edge_plot_type
case "nla.gfx.EdgeChordPlotMethod.COEFF"
main_title = positive_title;
if isfield(parameters, "lower_bound")
coefficient_min = parameters.lower_bound;
coefficient_max = parameters.p_value_plot_max;
end

case "nla.gfx.EdgeChordPlotMethod.COEFF_SPLIT"
main_title = negative_title;
positive_main_title = positive_title;
if isfield(parameters, "lower_bound")
coefficient_min = parameters.lower_bound;
coefficient_max = parameters.p_value_plot_max;
end

case "nla.gfx.EdgeChordPlotMethod.COEFF_BASE_SPLIT"
coefficient_min = obj.edge_test_result.coeff_range(1);
coefficient_max = obj.edge_test_result.coeff_range(2);
if isfield(parameters, "lower_bound")
coefficient_min = parameters.lower_bound;
coefficient_max = parameters.p_value_plot_max;
else
coefficient_min = obj.edge_test_result.coeff_range(1);
coefficient_max = obj.edge_test_result.coeff_range(2);
end

main_title = negative_title;
positive_main_title = positive_title;

case "nla.gfx.edgeChordPlotMethod.COEFF_BASE"
coefficient_min = obj.edge_test_result.coeff_range(1);
coefficient_max = obj.edge_test_result.coeff_range(2);
if isfield(parameters, "lower_bound")
coefficient_min = parameters.lower_bound;
coefficient_max = parameters.p_value_plot_max;
else
coefficient_min = obj.edge_test_result.coeff_range(1);
coefficient_max = obj.edge_test_result.coeff_range(2);
end

main_title = positive_title;

Expand All @@ -134,13 +173,19 @@ function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type)

clipped_values.v = obj.edge_test_result.prob.v;
significance_type = "nla.gfx.SigType.DECREASING";
coefficient_min = 0;
coefficient_max = obj.edge_test_result.prob_max;
if isfield(parameters, "lower_bound")
coefficient_min = parameters.lower_bound;
coefficient_max = parameters.p_value_plot_max;
else
coefficient_min = 0;
coefficient_max = obj.edge_test_result.prob_max;
end

insignificance = 1;
main_title = sprintf("Edge-level P-values (P < %g) (Within Significant Net-Pair)",...
obj.edge_test_result.prob_max);
end
coefficient_bounds = [coefficient_min, coefficient_max];

% Filtering/Thresholding out values
for network1 = 1:obj.network_atlas.numNets()
Expand All @@ -165,8 +210,8 @@ function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type)
obj.edge_plot_type == "nla.gfx.EdgeChordPlotMethod.COEFF_SPLIT" || obj.edge_plot_type == "nla.gfx.EdgeChordPlotMethod.COEFF_BASE_SPLIT"...
)
positive_chord_plotter = nla.gfx.chord.ChordPlot(obj.network_atlas, plot_axis, 450, clipped_values_positive,...
'direction', significance_type, 'chord_type', chord_type, 'color_map', color_map, 'lower_limit',...
coefficient_min, 'upper_limit', coefficient_max);
'direction', significance_type, 'chord_type', chord_type, 'color_map', parameters.color_map, 'lower_limit',...
coefficient_bounds(1), 'upper_limit', coefficient_bounds(2));
positive_chord_plotter.drawChords();
setTitle(plot_axis, positive_main_title);

Expand All @@ -177,12 +222,12 @@ function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type)
plot_axis.Visible = true;
end

chord_plotter = nla.gfx.chord.ChordPlot(obj.network_atlas, plot_axis, 450, clipped_values, 'chord_type', chord_type,...
'direction', significance_type, 'color_map', color_map, 'lower_limit', coefficient_min, 'upper_limit', coefficient_max);
chord_plotter.drawChords();
obj.chord_plotter = nla.gfx.chord.ChordPlot(obj.network_atlas, plot_axis, 450, clipped_values, 'chord_type', chord_type,...
'direction', significance_type, 'color_map', parameters.color_map, 'lower_limit', coefficient_bounds(1), 'upper_limit', coefficient_bounds(2));
obj.chord_plotter.drawChords();
setTitle(plot_axis, main_title);

colormap(plot_axis, color_map);
colormap(plot_axis, parameters.color_map);
color_bar = colorbar(plot_axis);
color_bar.Units = 'pixels';
color_bar.Location = 'east';
Expand All @@ -198,6 +243,108 @@ function generateEdgeChordFigure(obj, plot_figure, parameters, chord_type)
labels{tick + 1} = sprintf("%.2g", coefficient_min + (tick * ((coefficient_max - coefficient_min) / number_ticks)));
end
color_bar.TickLabels = labels;

settings_menu = uimenu(plot_figure, 'Text', 'Settings');
change_scale_option = uimenu(settings_menu,'Text','Change Scale');
change_scale_option.MenuSelectedFcn = {@obj.adjustScale, coefficient_bounds, plot_figure, parameters, chord_type};
change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
change_color_map.MenuSelectedFcn = {@obj.adjustColor, plot_figure, parameters, chord_type};
end

function adjustScale(obj, src, ~, bounds, plot_figure, parameters, chord_type)
chord_figure = src.Parent.Parent;
modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
[chord_figure.Position(1), chord_figure.Position(2), chord_figure.Position(3) / 3, chord_figure.Position(4) / 3]);

upper_limit_box = uicontrol('Style', 'edit', "Units", "pixels", 'Position', [90, 130, 100, 30], "String",...
bounds(2));
upper_limit_box.Position(4) = upper_limit_box.FontSize * 2;
lower_limit_box = uicontrol('Style', 'edit', "Units", "pixels", 'Position', [90, 100, 100, 30], "String",...
bounds(1));
lower_limit_box.Position(4) = lower_limit_box.FontSize * 2;

uicontrol('Style', 'text', 'String', 'Upper Limit', "Units", "pixels", 'Position',...
[upper_limit_box.Position(1) - 80, upper_limit_box.Position(2) - 2, 80, upper_limit_box.Position(4)]);
uicontrol('Style', 'text', 'String', 'Lower Limit', "Units", "pixels", 'Position',...
[lower_limit_box.Position(1) - 80, lower_limit_box.Position(2) - 2, 80, lower_limit_box.Position(4)]);

apply_button_position = [10, 10, 100, 30];
apply_button = uicontrol('String', 'Apply',...
"Callback", {@obj.applyScale, upper_limit_box, lower_limit_box, false, plot_figure, parameters, chord_type},...
"Units", "pixels",...
'Position', apply_button_position);

close_button_position = [apply_button.Position(1) + apply_button.Position(3) + 10,...
apply_button.Position(2), apply_button.Position(3), apply_button.Position(4)];
uicontrol('String', 'Close', 'Callback', @(~, ~)close(modal), "Units", "pixels", 'Position',...
close_button_position);
end

function adjustColor(obj, src, ~, plot_figure, parameters, chord_type)
chord_figure = src.Parent.Parent;
modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
[chord_figure.Position(1), chord_figure.Position(2), chord_figure.Position(3) / 2, chord_figure.Position(4) / 3]);

% Color Map selector
% Adapted from colormap-dropdown: https://www.mathworks.com/matlabcentral/fileexchange/43659-colormap-dropdown-menu

color_map_select = uicontrol('Style', 'popupmenu',...
'Position', [90, 130, 275, 30], "Units", "pixels",...
'FontName', 'Courier');
uicontrol("Style", "text", "string", "Colormaps", "Units", "pixels",...
"Position", [color_map_select.Position(1) - 80, color_map_select.Position(2) - 2, 80, color_map_select.Position(4)]);
initial_colors = 16;
colormap_html = {};
for colors = 1:numel(obj.colormap_choices)
colormap_function = str2func(strcat(strcat("@(x) ",lower(obj.colormap_choices{colors})), "(x)"));
CData = colormap_function(initial_colors);
new_html_start = '<HTML> ';
new_html = '';
for color_iterator = initial_colors:-1:1
hex_code = nla.gfx.rgb2hex([CData(color_iterator, 1), CData(color_iterator, 2),...
CData(color_iterator, 3)]);
new_html = [new_html '<FONT bgcolor="' hex_code ' "color="' hex_code '">__</FONT>'];
end
new_html_end = [new_html ' </HTML>'];
new_html = [new_html_start new_html_end];
colormap_html = [colormap_html; new_html];
end

if ~isfield(parameters, "color_map_name")
parameters.color_map_name = 1;
end
set(color_map_select, "Value", parameters.color_map_name, "String", colormap_html);

apply_button_position = [10, 10, 100, 30];
apply_button = uicontrol('String', 'Apply',...
"Callback", {@obj.applyScale, false, false, color_map_select, plot_figure, parameters, chord_type},...
"Units", "pixels",...
'Position', apply_button_position);

close_button_position = [apply_button.Position(1) + apply_button.Position(3) + 10,...
apply_button.Position(2), apply_button.Position(3), apply_button.Position(4)];
uicontrol('String', 'Close', 'Callback', @(~, ~)close(modal), "Units", "pixels", 'Position',...
close_button_position);
end

function applyScale(obj, src, ~, upper_limit_box, lower_limit_box, color_map, plot_figure, parameters, chord_type)

if ~isequal(upper_limit_box, false)
parameters.p_value_plot_max = str2double(get(upper_limit_box, "String"));
parameters.lower_bound = str2double(get(lower_limit_box, "String"));
end

if ~isequal(color_map, false)
color_map = get(color_map, "Value");
color_map_name = str2func(lower(obj.colormap_choices{color_map}));
parameters.color_map = color_map_name(1000);
parameters.color_map_name = color_map;
end

obj.generateChordFigure(parameters, chord_type, plot_figure)

close(plot_figure);
close(src.Parent);
end
end
end
Binary file modified +nla/+net/+result/+plot/NetworkTestPlotApp.mlapp
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2 changes: 1 addition & 1 deletion +nla/+net/+result/+plot/NetworkTestPlotApp_exported.m
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Original file line number Diff line number Diff line change
Expand Up @@ -285,7 +285,7 @@ function drawChords(app, event)
chord_plotter = nla.net.result.chord.ChordPlotter(app.edge_test_options.net_atlas, app.edge_test_result);

probability_parameters.edge_chord_plot_method = app.EdgeChordPlotTypeDropDown.Value;
chord_plotter.generateChordFigure(probability_parameters, plot_type)
chord_plotter.generateChordFigure(probability_parameters, plot_type, false)
end

% Value changed function: ColormapDropDown,
Expand Down
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