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

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Merged
pollaro merged 9 commits into from
Jul 27, 2026
Merged

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

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884e754
added scaling and colormap choice to chords
pollaro Jul 2, 2026
b94a697
hopefully centering plots together
pollaro Jul 6, 2026
dcbb1f8
Exported mlapp files
actions-user Jul 6, 2026
90c95b6
edge chord scaling
pollaro Jul 6, 2026
af8e21f
moved color and scale modals to seperate functions
pollaro Jul 20, 2026
0880c3d
trying to put colormap select and scale to non-app matrix plot
pollaro Jul 20, 2026
1d31a76
added lots of str2double
pollaro Jul 27, 2026
e7ae4d3
added scaling setting for edge matrix plot
pollaro Jul 27, 2026
04a90c8
Exported mlapp files
actions-user Jul 27, 2026
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2 changes: 1 addition & 1 deletion +nla/+edge/+result/Base.m
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

fig = nla.gfx.createFigure();
matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
'upper_limit', obj.coeff_range(2));
'upper_limit', obj.coeff_range(2), 'app_plot', false);
matrix_plot.displayImage();
w = matrix_plot.image_dimensions("image_width");
h = matrix_plot.image_dimensions("image_height");
Expand Down
60 changes: 51 additions & 9 deletions +nla/+gfx/+plots/MatrixPlot.m
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Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
current_settings % the settings for the plot (upper, lower, scale)
display_legend
p_value_max
app_plot % Used when called for FC Avg
end

properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
addParameter(matrix_input_parser, 'p_value_max', 0.05)
addParameter(matrix_input_parser, 'p_value_max', 0.05);
addParameter(matrix_input_parser, 'app_plot', true, @islogical)

parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
for property = properties
obj.(property{1}) = matrix_input_parser.Results.(property{1});
if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
'HorizontalAlignment', 'center');
end

if isequal(obj.app_plot, false)
settings_menu = uimenu(obj.figure, 'Text', 'Settings');
change_scale_option = uimenu(settings_menu,'Text','Change Scale');
change_scale_option.MenuSelectedFcn = {...
@obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
false...
};
change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
end

obj.fixRendering();
hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
obj.color_bar.Ticks = [];

color_map = color_map_select;
if ~isstring(color_map_select) && ~ischar(color_map_select)
if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
color_map = get(color_map_select, "Value");
color_map = obj.colormap_choices{color_map};
end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
if isnumeric(upper_limit_box)
obj.upper_limit = upper_limit_box;
else
obj.upper_limit = get(upper_limit_box, "String");
obj.upper_limit = get(upper_limit_box, 'String');
end

if isnumeric(lower_limit_box)
obj.lower_limit = lower_limit_box;
else
obj.lower_limit = get(lower_limit_box, "String");
obj.lower_limit = get(lower_limit_box, 'String');
end

if isstring(obj.upper_limit) || ischar(obj.upper_limit)
obj.upper_limit = str2double(obj.upper_limit);
end
if isstring(obj.lower_limit) || ischar(obj.lower_limit)
obj.lower_limit = str2double(obj.lower_limit);
end

if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
if ~isequal(color_map, false)
new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
else
new_color_map = obj.color_map;
end
obj.plot_scale = new_scale;
elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
image_height = image_height + 20;
end

% colorbar margins
% colorbar marginsobj
if obj.draw_colorbar
image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
initial_render = false;
upper_value = varargin{2};
lower_value = varargin{1};
if isstring(upper_value)
if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
upper_value = str2double(upper_value);
end
if isstring(lower_value)
if isstring(lower_value) || ischar(lower_value)
lower_value = str2double(lower_value);
end
end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
end

function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
end

function adjustColor(obj, src, ~, plot_figure, parameters, ~)
nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
end

function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
% This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
if isequal(upper_limit_box, false)
upper_limit_box = obj.upper_limit;
lower_limit_box = obj.lower_limit;
end
obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
end
end
end
46 changes: 46 additions & 0 deletions +nla/+gfx/colorSelector.m
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
original_figure = src.Parent.Parent;
modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
[original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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
28 changes: 28 additions & 0 deletions +nla/+gfx/scaleSelector.m
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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
original_figure = src.Parent.Parent;
modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
[original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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
3 changes: 2 additions & 1 deletion +nla/+inputField/NetworkAtlasFuncConn.m
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
fc_avg = copy(obj.func_conn);
fc_avg.v = mean(fc_avg.v, 2);
fig_l = nla.gfx.createFigure();

matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
nla.gfx.FigSize.LARGE);
nla.gfx.FigSize.LARGE, "app_plot", false);
fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
matrix_plot.displayImage();
Expand Down
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
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var __m = "github.com";
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[NET-314] Scaling and color choice on chord plots#160

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 Merged

pollaro
merged 9 commits into

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Jul 27, 2026
 Merged


[NET-314] Scaling and color choice on chord plots
#160
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884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

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Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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

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 Merged

pollaro
merged 9 commits into

from

Jul 27, 2026
 Merged


[NET-314] Scaling and color choice on chord plots
#160
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884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

pollaro
merged 9 commits into

from

Jul 27, 2026
 Merged


[NET-314] Scaling and color choice on chord plots
#160
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


9 commits


Select commit
Hold shift + click to select a range
884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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Filter by extension
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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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

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 Merged

pollaro
merged 9 commits into

from

Jul 27, 2026
 Merged


[NET-314] Scaling and color choice on chord plots
#160
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884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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

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 Merged

pollaro
merged 9 commits into

from

Jul 27, 2026
 Merged


[NET-314] Scaling and color choice on chord plots
#160
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884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
Loading
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

pollaro
merged 9 commits into

from

Jul 27, 2026
 Merged


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


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Hold shift + click to select a range
884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

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Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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

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 Merged

pollaro
merged 9 commits into

from

Jul 27, 2026
 Merged


[NET-314] Scaling and color choice on chord plots
#160
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884e754

added scaling and colormap choice to chords


pollaro Jul 2, 2026
b94a697

hopefully centering plots together


pollaro Jul 6, 2026
dcbb1f8

Exported mlapp files


actions-user Jul 6, 2026
90c95b6

edge chord scaling


pollaro Jul 6, 2026
af8e21f

moved color and scale modals to seperate functions


pollaro Jul 20, 2026
0880c3d

trying to put colormap select and scale to non-app matrix plot


pollaro Jul 20, 2026
1d31a76

added lots of str2double


pollaro Jul 27, 2026
e7ae4d3

added scaling setting for edge matrix plot


pollaro Jul 27, 2026
04a90c8

Exported mlapp files


actions-user Jul 27, 2026

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2 changes: 1 addition & 1 deletion
+nla/+edge/+result/Base.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)

 fig = nla.gfx.createFigure();
 matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
 'upper_limit', obj.coeff_range(2));
 'upper_limit', obj.coeff_range(2), 'app_plot', false);
 matrix_plot.displayImage();
 w = matrix_plot.image_dimensions("image_width");
 h = matrix_plot.image_dimensions("image_height");
Expand Down

60 changes: 51 additions & 9 deletions
+nla/+gfx/+plots/MatrixPlot.m

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Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@
 current_settings % the settings for the plot (upper, lower, scale)
 display_legend
 p_value_max
 app_plot % Used when called for FC Avg
 end

 properties (Dependent)
Expand DownExpand Up@@ -112,12 +113,13 @@
 addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
 addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
 addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
 addParameter(matrix_input_parser, 'p_value_max', 0.05)
 addParameter(matrix_input_parser, 'p_value_max', 0.05);
 addParameter(matrix_input_parser, 'app_plot', true, @islogical)

 parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
 properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
 'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
 for property = properties
 obj.(property{1}) = matrix_input_parser.Results.(property{1});
 if property{1} == "marked_networks"
Expand DownExpand Up@@ -182,6 +184,18 @@ function displayImage(obj)
 'HorizontalAlignment', 'center');
 end

 if isequal(obj.app_plot, false)
 settings_menu = uimenu(obj.figure, 'Text', 'Settings');
 change_scale_option = uimenu(settings_menu,'Text','Change Scale');
 change_scale_option.MenuSelectedFcn = {...
 @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
 struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
 false...
 };
 change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
 change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
 end

 obj.fixRendering();
 hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.

Expand All@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 obj.color_bar.Ticks = [];

 color_map = color_map_select;
 if ~isstring(color_map_select) && ~ischar(color_map_select)
 if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
 color_map = get(color_map_select, "Value");
 color_map = obj.colormap_choices{color_map};
 end
Expand All@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 if isnumeric(upper_limit_box)
 obj.upper_limit = upper_limit_box;
 else
 obj.upper_limit = get(upper_limit_box, "String");
 obj.upper_limit = get(upper_limit_box, 'String');
 end

 if isnumeric(lower_limit_box)
 obj.lower_limit = lower_limit_box;
 else
 obj.lower_limit = get(lower_limit_box, "String");
 obj.lower_limit = get(lower_limit_box, 'String');
 end

 if isstring(obj.upper_limit) || ischar(obj.upper_limit)
 obj.upper_limit = str2double(obj.upper_limit);
 end
 if isstring(obj.lower_limit) || ischar(obj.lower_limit)
 obj.lower_limit = str2double(obj.lower_limit);
 end

 if ~isstring(obj.plot_scale)
Expand All@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
 discrete_colors = NetworkResultPlotParameter().default_discrete_colors;

 if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 if ~isequal(color_map, false)
 new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
 else
 new_color_map = obj.color_map;
 end
 obj.plot_scale = new_scale;
 elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
Expand DownExpand Up@@ -337,7 +362,7 @@ function removeLegend(obj)
 image_height = image_height + 20;
 end

 % colorbar margins
 % colorbar marginsobj
 if obj.draw_colorbar
 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
 end
Expand DownExpand Up@@ -435,10 +460,10 @@ function addCallback(obj, x)
 initial_render = false;
 upper_value = varargin{2};
 lower_value = varargin{1};
 if isstring(upper_value)
 if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
 upper_value = str2double(upper_value);
 end
 if isstring(lower_value)
 if isstring(lower_value) || ischar(lower_value)
 lower_value = str2double(lower_value);
 end
 end
Expand DownExpand Up@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
 obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
 end

 function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
 nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
 end

 function adjustColor(obj, src, ~, plot_figure, parameters, ~)
 nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
 end

 function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
 % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
 if isequal(upper_limit_box, false)
 upper_limit_box = obj.upper_limit;
 lower_limit_box = obj.lower_limit;
 end
 obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
 end
 end
end

46 changes: 46 additions & 0 deletions
+nla/+gfx/colorSelector.m

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_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(color_choices)
 colormap_function = str2func(strcat(strcat("@(x) ",lower(color_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", {callback_function, 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

28 changes: 28 additions & 0 deletions
+nla/+gfx/scaleSelector.m

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,28 @@
function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
 original_figure = src.Parent.Parent;
 modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
 [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_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", {callback_function, 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

3 changes: 2 additions & 1 deletion
+nla/+inputField/NetworkAtlasFuncConn.m

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
 fc_avg = copy(obj.func_conn);
 fc_avg.v = mean(fc_avg.v, 2);
 fig_l = nla.gfx.createFigure();

 matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
 nla.gfx.FigSize.LARGE);
 nla.gfx.FigSize.LARGE, "app_plot", false);
 fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
 fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
 matrix_plot.displayImage();
Expand Down
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