Placing transparent rectangles on top of a plot

Hey all,

I am trying to place several rectanges over a plot (wavelet coherence) but am struggling to do so.

I have been using the following code below, which has been creating the plots successfully but the rectangles do not seem to appear on the plots.

I would be so grateful for a helping hand! :)

Please let me know if there's anymore/example data I can provide.

       wcoherence(data1,data2);
        ax = gca;
        final_onset = dataTable.onsetsWC(end);
        final_duration = dataTable.durationsWC(end);
        max_x_limit = final_onset + final_duration;
        xlim([0, max_x_limit]);
        for i = 1:height(dataTable)
            onset = dataTable.onsetsWC(i);
            duration = dataTable.durationsWC(i);
            trialType = dataTable.Trialtype(i);
            if strcmp(trialType, 'Chase')
                barColor = [1, 0, 0, 1]; 
            elseif strcmp(trialType, 'Follow')
                barColor = [0, 1, 0, 1]; 
            end
            rectangle(ax, 'Position', [onset, 0, duration, 1], 'FaceColor', barColor, 'EdgeColor', 'none');
        end
        figure_title = sprintf('Dyad-%d-Channel-%d', p, j);
        set(gcf, 'Name', figure_title);
        save_path = 'C:\Users\emre.yavuz\Desktop\DataGLM\Waveletcoherence';
        save_name = sprintf('Dyad_%d_Channel_%d.fig', p, j);
        saveas(gcf, fullfile(save_path, save_name));

Answer 1

[Voss]

It's hard to say for sure what the problem is without the data, but one problem might be that the axes Y-Limits are outside where the rectangles are. The rectangles are all from y=0 to y=1, but the axes Y-Limits may be something else.

For example, with the made up data below, wcoherence creates an axes whose Y-Limits are approximately [-5.19, -1.44] (in spite of the fact that the y-tick labels suggest the Y-Limits are approximately [0.03, 0.3]).

To fix that problem, use the actual Y-Limits as the upper and lower limits of the rectangles. One way to do that is shown below. (I also included a FaceAlpha of 0.5 in the rectangles because otherwise they had no transparency.)

data1 = rand(100,1);
data2 = rand(100,1);

onsetsWC = [20;30;50;80];
durationsWC = [5;7.5;3;10];
Trialtype = {'Chase';'Follow';'Chase';'Follow'};
dataTable = table(onsetsWC,durationsWC,Trialtype);

wcoherence(data1,data2)

ax = gca;

ax.YLim % YLim is not what you might expect from looking at the plot

ans = 1x2

-5.1911 -1.4411

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final_onset = dataTable.onsetsWC(end);
final_duration = dataTable.durationsWC(end);
max_x_limit = final_onset + final_duration;
xlim([0, max_x_limit]);

% use the actual axes YLim in defining the rectangles
y_lim = ax.YLim;
dy_lim = y_lim(2)-y_lim(1);

for i = 1:height(dataTable)
    onset = dataTable.onsetsWC(i);
    duration = dataTable.durationsWC(i);
    trialType = dataTable.Trialtype(i);
    if strcmp(trialType, 'Chase')
        barColor = [1, 0, 0, 1]; 
    elseif strcmp(trialType, 'Follow')
        barColor = [0, 1, 0, 1]; 
    end
    rectangle(ax, 'Position', [onset, y_lim(1), duration, dy_lim], ...
        'FaceColor', barColor, 'EdgeColor', 'none', 'FaceAlpha', 0.5);
end

[Emre]

Thank you so so much for your help - that worked! :)

One thing - the FaceAlpha property wasn't recognised by the rectangle function, and so I had to change the transparency when I specified the red and green colours as follows:

        wcoherence(data1, data2);
        ax = gca;
        final_onset = dataTable.onsetsWC(end);
        final_duration = dataTable.durationsWC(end);
        max_x_limit = final_onset + final_duration;
        xlim([0, max_x_limit]);
        y_lim = ax.YLim;
        dy_lim = y_lim(2)-y_lim(1);
        for i = 1:height(dataTable)
            onset = dataTable.onsetsWC(i);
            duration = dataTable.durationsWC(i);
            trialType = dataTable.Trialtype(i);
            if strcmp(trialType, 'Chase')
                barColor = [1, 0, 0, 0.5]; %50 transparency 
            elseif strcmp(trialType, 'Follow')
                barColor = [0, 1, 0, 0.5]; %50% transparency 
            end
            rectangle(ax, 'Position', [onset, y_lim(1), duration, dy_lim], ...
        'FaceColor', barColor, 'EdgeColor', 'black');
        end
        figure_title = sprintf('Dyad-%d-Channel-%d', p, j);
        set(gcf, 'Name', figure_title);
        save_path = 'C:\Users\emre.yavuz\Desktop\DataGLM\Waveletcoherence';
        save_name = sprintf('Dyad_%d_Channel_%d.fig', p, j);
        saveas(gcf, fullfile(save_path, save_name));

[Voss]

You're welcome! Glad it's working.

"the FaceAlpha property wasn't recognised by the rectangle function, and so I had to change the transparency when I specified the red and green colours"

Strange, I had the opposite problem (which is why I changed it to use FaceAlpha). You can see here the rectangles are completely opaque (apparently not respecting the alpha as the 4th element of the color). I guess it's due to different versions of MATLAB.

        data1 = rand(100,1);
        data2 = rand(100,1);
        onsetsWC = [20;30;50;80];
        durationsWC = [5;7.5;3;10];
        Trialtype = {'Chase';'Follow';'Chase';'Follow'};
        dataTable = table(onsetsWC,durationsWC,Trialtype);        
        
        wcoherence(data1, data2);
        ax = gca;
        final_onset = dataTable.onsetsWC(end);
        final_duration = dataTable.durationsWC(end);
        max_x_limit = final_onset + final_duration;
        xlim([0, max_x_limit]);
        y_lim = ax.YLim;
        dy_lim = y_lim(2)-y_lim(1);
        for i = 1:height(dataTable)
            onset = dataTable.onsetsWC(i);
            duration = dataTable.durationsWC(i);
            trialType = dataTable.Trialtype(i);
            if strcmp(trialType, 'Chase')
                barColor = [1, 0, 0, 0.5]; %50 transparency 
            elseif strcmp(trialType, 'Follow')
                barColor = [0, 1, 0, 0.5]; %50% transparency 
            end
            rectangle(ax, 'Position', [onset, y_lim(1), duration, dy_lim], ...
                'FaceColor', barColor, 'EdgeColor', 'black');
        end