dynamic histogram plots

Julie-Fabre · Oct 13, 2024 · 46d9225 · 46d9225
1 parent d2652dd
commit 46d9225
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Showing 8 changed files with 456 additions and 845 deletions.
diff --git a/+bc/+qm/plotGlobalQualityMetric.asv b/+bc/+qm/plotGlobalQualityMetric.asv
diff --git a/+bc/+qm/plotGlobalQualityMetric.m b/+bc/+qm/plotGlobalQualityMetric.m
diff --git a/+bc/+qm/qualityParamValues.m b/+bc/+qm/qualityParamValues.m
@@ -117,7 +117,7 @@
     param.waveformBaselineWindowStart = 20;
     param.waveformBaselineWindowStop = 30; % in samples 
 end
-param.minThreshDetectPeaksTroughs = 0.1; % this is multiplied by the max value 
+param.minThreshDetectPeaksTroughs = 0.2; % this is multiplied by the max value 
     % in a units waveform to give the minimum prominence to detect peaks using
     % matlab's findpeaks function.
 param.normalizeSpDecay = 1; % whether to normalize spatial decay points relative to 

diff --git a/+bc/+qm/runAllQualityMetrics.asv b/+bc/+qm/runAllQualityMetrics.asv
diff --git a/+bc/+qm/waveformShape.m b/+bc/+qm/waveformShape.m
@@ -146,8 +146,11 @@
     linearFit = param.spDecayLinFit;
     [spatialDecaySlope, spatialDecayFit, spatialDecayPoints, spatialDecayPoints_loc, estimatedUnitXY] = ...
         bc.qm.helpers.getSpatialDecay(templateWaveforms, thisUnit, maxChannel, channelPositions, linearFit, param.normalizeSpDecay, param.computeSpatialDecay);
-
-spatialDecayFit_1 = spatialDecayFit(1);
+    if linearFit
+        spatialDecayFit_1 = spatialDecayFit(2);
+    else
+        spatialDecayFit_1 = spatialDecayFit(1);
+    end
     % (get waveform baseline fraction)
     if ~isnan(waveformBaselineWindow(1))
         waveformBaseline = max(abs(thisWaveform(waveformBaselineWindow(1): ...

diff --git a/+bc/+viz/unitQualityGUI_synced.m b/+bc/+viz/unitQualityGUI_synced.m
@@ -1,5 +1,7 @@
 
 %% unit quality gui: plot various quality metric plots for single units
+% This function is very messy - don't attempt to modify. Send me an email or raise an issue :) 
+% 
 % toggle between units with the right and left arrows
 % the slowest part by far of this is plotting the raw data, need to figure out how
 % to make this faster
@@ -130,9 +132,35 @@ function initializePlot(unitQualityGuiHandle, ephysData, qMetric, unitType, uniq
     numCols = ceil(numSubplots/numRows);
 
     % Color matrix setup
-    colorMtx = [bc.viz.colors(15); bc.viz.colors(15)];
-    colorMtx = [colorMtx(1:21, :, :), repmat(0.7, 21, 1)]; % make 70% transparent
-    colorMtx = colorMtx([1:4:end, 2:4:end, 3:4:end, 4:4:end], :); % shuffle colors
+    red_colors = [
+    0.8627 0.0784 0.2353;  % Crimson
+    1.0000 0.1412 0.0000;  % Scarlet
+    0.7255 0.0000 0.0000;  % Cherry
+    0.5020 0.0000 0.1255;  % Burgundy
+    0.5020 0.0000 0.0000;  % Maroon
+    0.8039 0.3608 0.3608   % Indian Red
+];
+
+    blue_colors = [
+    0.2549 0.4118 0.8824;  % Royal Blue
+    0.0000 0.0000 0.5020   % Navy Blue
+];
+    % Color matrix setup
+     darker_yellow_orange_colors = [
+    0.7843 0.7843 0.0000;  % Dark Yellow
+    0.8235 0.6863 0.0000;  % Dark Golden Yellow
+    0.8235 0.5294 0.0000;  % Dark Orange
+    0.8039 0.4118 0.3647;  % Dark Coral
+    0.8235 0.3176 0.2275;  % Dark Tangerine
+    0.8235 0.6157 0.6510;  % Dark Salmon
+    0.7882 0.7137 0.5765;  % Dark Goldenrod
+    0.8235 0.5137 0.3922;  % Dark Light Coral
+    0.7569 0.6196 0.0000;  % Darker Goldenrod
+    0.8235 0.4510 0.0000   % Darker Orange
+];
+
+
+    colorMtx = [red_colors; blue_colors;darker_yellow_orange_colors]; % shuffle colors
 
     %sgtitle([num2str(sum(unitType == 1)), ' single units, ', num2str(sum(unitType == 2)), ' multi-units, ', ...
     %    num2str(sum(unitType == 0)), ' noise units, ', num2str(sum(unitType == 3)), ' non-somatic units.']);
@@ -148,9 +176,9 @@ function initializePlot(unitQualityGuiHandle, ephysData, qMetric, unitType, uniq
 
         % Plot histogram
         if i > 2
-            h = histogram(ax, metricData, 40, 'FaceColor', colorMtx(i, 1:3), 'FaceAlpha', colorMtx(i, 4), 'Normalization', 'probability');
+            h = histogram(ax, metricData, 40, 'FaceColor', colorMtx(i, 1:3),  'Normalization', 'probability');
         else
-            h = histogram(ax, metricData, 'FaceColor', colorMtx(i, 1:3), 'FaceAlpha', colorMtx(i, 4), 'Normalization', 'probability');
+            h = histogram(ax, metricData, 'FaceColor', colorMtx(i, 1:3), 'Normalization', 'probability');
         end
         binsize_offset = h.BinWidth/2;
         % Add horizontal lines instead of rectangles

diff --git a/+bc/+viz/upSetPlot.m b/+bc/+viz/upSetPlot.m
@@ -1,4 +1,4 @@
-function upSetPlot(data, labels, figH)
+function upSetPlot(data, labels, figH, setSizeColor)
 % More info on UpSet plots in the original publication:
 % Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot,
 % Hanspeter Pfister. UpSet: Visualization of Intersecting Sets
@@ -10,15 +10,16 @@ function upSetPlot(data, labels, figH)
 % written by Zhaoxu Liu / slandarer
 
 if nargin < 3 || isempty(figH)
-    figH = figure('Units', 'normalized', 'Position', [.3, .2, .5, .63], 'Color', [1, 1, 1]);
-
+    figH = figure('Units', 'normalized', 'Position', [.2, .2, 1, .63], 'Color', [1, 1, 1]);
 end
+
 % set colors 
-intxColor = [66, 182, 195] ./ 255;
+intxColor = [0, 0, 0];
+if nargin < 4 || isempty(setSizeColor)
 setSizeColor = bc.viz.colors(size(data,2));
+end
 lineColor = [61, 58, 61] ./ 255;
 
-
 % get probabilities & groups 
 pBool = abs(dec2bin((1:(2^size(data, 2) - 1))')) - 48;
 [pPos, ~] = find(((pBool * (1 - data')) | ((1 - pBool) * data')) == 0);
@@ -36,22 +37,22 @@ function upSetPlot(data, labels, figH)
 %% create figure and subplots
 axI = axes('Parent', figH);
 hold on;
-set(axI, 'Position', [.33, .35, .655, .61], 'LineWidth', 1.2, 'Box', 'off', 'TickDir', 'out', ...
+set(axI, 'Position', [.45, .35, .53, .48], 'LineWidth', 1.2, 'Box', 'off', 'TickDir', 'out', ...
     'FontName', 'Arial', 'FontSize', 12, 'XTick', [], 'XLim', [0, length(pType) + 1])
 axI.YLabel.String = 'Intersection Size';
 axI.YLabel.FontSize = 16;
-%
+
 axS = axes('Parent', figH);
 hold on;
-set(axS, 'Position', [.01, .08, .245, .26], 'LineWidth', 1.2, 'Box', 'off', 'TickDir', 'out', ...
+set(axS, 'Position', [.2, .08, .2, .26], 'LineWidth', 1.2, 'Box', 'off', 'TickDir', 'out', ...
     'FontName', 'Arial', 'FontSize', 12, 'YColor', 'none', 'YLim', [.5, size(data, 2) + .5], ...
     'YAxisLocation', 'right', 'XDir', 'reverse', 'YTick', [])
 axS.XLabel.String = 'Set Size';
 axS.XLabel.FontSize = 16;
-%
+
 axL = axes('Parent', figH);
 hold on;
-set(axL, 'Position', [.33, .08, .655, .26], 'YColor', 'none', 'YLim', [.5, size(data, 2) + .5], 'XColor', 'none', 'XLim', axI.XLim)
+set(axL, 'Position', [.45, .08, .53, .26], 'YColor', 'none', 'YLim', [.5, size(data, 2) + .5], 'XColor', 'none', 'XLim', axI.XLim)
 
 %% plot interaction bar plots 
 barHdlI = bar(axI, pCount);
@@ -69,19 +70,21 @@ function upSetPlot(data, labels, figH)
 for i = 1:length(pType)
     barHdlI.CData(i, :) = intxColor(i, :);
 end
-text(axI, 1:length(pType), pCount, string(pCount), 'HorizontalAlignment', 'center', ...
-    'VerticalAlignment', 'bottom', 'FontName', 'Arial', 'FontSize', 12, 'Color', [61, 58, 61]./255)
+%text(axI, 1:length(pType), pCount, string(pCount), 'HorizontalAlignment', 'center', ...
+%    'VerticalAlignment', 'bottom', 'FontName', 'Arial', 'FontSize', 12, 'Color', [61, 58, 61]./255)
 
 %% plot set sizes 
 barHdlS = barh(axS, sCount, 'BarWidth', .6);
 barHdlS.EdgeColor = 'none';
 barHdlS.BaseLine.Color = 'none';
+
+% Adjust label position
 for i = 1:size(data, 2)
-    annotation('textbox', [(axS.Position(1) + axS.Position(3) + axI.Position(1)) / 2 - .02, ...
-        axS.Position(2) + axS.Position(4) ./ size(data, 2) .* (i - .5) - .02, .04, .04], ...
-        'String', labels{sInd(i)}, 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle', ...
-        'FitBoxToText', 'on', 'LineStyle', 'none', 'FontName', 'Arial', 'FontSize', 13)
+    text(axS, max(sCount), i, labels{sInd(i)}, 'HorizontalAlignment', 'right', ...
+        'VerticalAlignment', 'middle', 'FontName', 'Arial', 'FontSize', 13, ...
+        'Color', [0.2, 0.2, 0.2]);
 end
+
 if size(setSizeColor, 1) == 1
     setSizeColor = [setSizeColor; setSizeColor];
 end
@@ -97,8 +100,11 @@ function upSetPlot(data, labels, figH)
     barHdlS.CData(i, :) = setSizeColor(i, :);
     sstr{i} = [num2str(sCount(i)), ' '];
 end
-text(axS, sCount, 1:size(data, 2), sstr, 'HorizontalAlignment', 'right', ...
-    'VerticalAlignment', 'middle', 'FontName', 'Arial', 'FontSize', 12, 'Color', [61, 58, 61]./255)
+%text(axS, sCount + max(sCount)*0.02, 1:size(data, 2), sstr, 'HorizontalAlignment', 'left', ...
+%    'VerticalAlignment', 'middle', 'FontName', 'Arial', 'FontSize', 12, 'Color', [61, 58, 61]./255)
+
+% Adjust x-axis limits to accommodate labels
+axS.XLim = [-max(sCount)*0.15, max(sCount) * 1.5];
 
 %% plot interaction details 
 patchColor = [248, 246, 249; 255, 254, 255] ./ 255;