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[NET-319] Fix scale changes on Tri-Matrix for non network plots #170

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Merged
pollaro merged 3 commits into from
Aug 31, 2026
Merged

[NET-319] Fix scale changes on Tri-Matrix for non network plots #170

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02516a2
add option that whites out scale over/under scale
pollaro Aug 31, 2026
d7096fa
fix all get color map values
pollaro Aug 31, 2026
fe637be
fix getlogcolormap inputs
pollaro Aug 31, 2026
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4 changes: 2 additions & 2 deletions +nla/+gfx/+plots/MatrixPlot.m
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Original file line number Diff line number Diff line change
Expand Up @@ -261,13 +261,13 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_

if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
if ~isequal(color_map, false)
new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map, obj.app_plot);
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);
new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map, obj.app_plot);
obj.plot_scale = new_scale;
else
color_map_name = str2func(lower(color_map));
Expand Down
18 changes: 11 additions & 7 deletions +nla/+net/+result/NetworkResultPlotParameter.m
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@
switch obj.updated_test_options.prob_plot_method
case "LOG"
color_map = nla.net.result.NetworkResultPlotParameter.getLogColormap(obj.default_discrete_colors,...
statistic_input, p_value_max);
statistic_input, p_value_max, true);
% Here we take a -log10 and change the maximum value to show on the plot
case "NEGATIVE_LOG_10"
color_map = parula(obj.default_discrete_colors);
Expand All @@ -97,7 +97,7 @@
significance_type = "nla.gfx.SigType.INCREASING";
otherwise
color_map = nla.net.result.NetworkResultPlotParameter.getColormap(obj.default_discrete_colors,...
p_value_max);
p_value_max, true);
end
else
ranking_statistic = obj.network_test_results.ranking_statistic;
Expand All @@ -111,7 +111,7 @@
% color_map
significance_type = "nla.gfx.SigType.DECREASING";
color_map = nla.net.result.NetworkResultPlotParameter.getColormap(obj.default_discrete_colors,...
p_value_plot_max);
p_value_plot_max, true);
end

% callback function for brain image.
Expand Down Expand Up @@ -225,7 +225,7 @@ function brainFigureButtonCallback(network1, network2)
end

methods(Static)
function color_map = getLogColormap(default_discrete_colors, probabilities_input, p_value_max, color_map)
function color_map = getLogColormap(default_discrete_colors, probabilities_input, p_value_max, color_map, white_out)
log_minimum = log10(min(nonzeros(probabilities_input.v)));
log_minimum = max([-40, log_minimum]);

Expand All @@ -240,13 +240,15 @@ function brainFigureButtonCallback(network1, network2)
if p_value_max ~= 0
color_map = flip(color_map_base(ceil(logspace(log_minimum, 0, default_discrete_colors) .*...
default_discrete_colors), :));
color_map = [color_map; default_color_map];
if white_out
color_map = [color_map; default_color_map];
end
else
color_map = default_color_map;
end
end

function color_map = getColormap(default_discrete_colors, p_value_max, color_map)
function color_map = getColormap(default_discrete_colors, p_value_max, color_map, white_out)
color_map_base = parula(default_discrete_colors);
if nargin > 2
color_map_name = str2func(lower(color_map));
Expand All @@ -258,7 +260,9 @@ function brainFigureButtonCallback(network1, network2)
color_map = default_color_map;
else
color_map = flip(color_map_base);
color_map = [color_map; default_color_map];
if white_out
color_map = [color_map; default_color_map];
end
end
end
end
Expand Down
2 changes: 1 addition & 1 deletion +nla/+qualityControl/checkNormalityWithKS.m
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ function qcKSOutput(ks_result_p_value, edge_test_options, remove_index)
[~, p_value_max] = network_test_options.fdr_correction.correct(network_atlas, edge_test_options, ks_result_p_value);

color_map = nla.net.result.NetworkResultPlotParameter.getColormap(default_discrete_colors,...
p_value_max);
p_value_max, true);

fig = nla.gfx.createFigure();
% Also remember to move this in read the docs
Expand Down
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