function [] =  plotOpticalTraces_transients_compare(compositeTrace1, threshold, transients, dtrans1, dtrans2, usecells, Hz, medfil, meanframe)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plots a set of temporal traces (intended to be fluorescence or DF/F) along 
% with markers to denote when important events (ie. calcium transients)
% occur. 
% Inputs:
%     - compositeTrace: Mx#Neuron temporal traces of the fluorescence
%     - threshold: threshold used to determine whether a transient occured
%     or not
%     - transients: Cell array containing the indexes of the true
%     transients
%     - dtrans1: cell array containing the indexes of the transients identified by method 1
%     - dtrans2: cell array containing the indexes of the transients
%     identified by method 2
%     - Usecells: Vector of the temporal traces to plot
%     - Hz: The imaging rate
%     - medfil: number of frames to use for the moving median
%     - meanframe: number of frames to use for the short moving average
%     filter
% Outputs: (none)
%     -
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

[tracea, ~] = size(compositeTrace1);
pace = 1/Hz;
 time = (1:tracea)*pace;
 raise = 0;
for fn = 1:length(usecells)
    i = usecells(fn);
    t = compositeTrace1(:, i);
    dfF = movmean(t, meanframe);

    mindf = min(dfF);
    dfF = dfF-mindf+raise;
    plot(time, dfF, 'k')
    if fn == 1
        hold on
    end
    medtrace= movmedian(dfF, medfil);
    
    yline(threshold(i)+median(dfF), 'k--')
    plot(time, threshold(i)+medtrace, 'r--');

    trans = transients{usecells(fn)};
    plot(trans*pace, ones(size(trans))*raise+range(dfF), 'k*')
   
    trans = dtrans1{usecells(fn)};
    if ~isempty(trans)
        plot(trans*pace, ones(size(trans))*raise+range(dfF)+0.01, 'ko')
    end
    
    trans = dtrans2{usecells(fn)};
    if ~isempty(trans)
        plot(trans*pace, ones(size(trans))*raise+range(dfF)+0.02, 'rv')
    end
    raise = raise+range(dfF)+0.05;
    if i == 1
        legend({'Trace 1', 'Threshold', 'Moving threshold', 'GT', 'Transients 1', 'Transients 2'}, 'AutoUpdate', 'off');
    end
end
hold off
xlabel('Time(s)');
ylabel('Cell Number');


set(gca, 'FontName', 'Arial', 'FontSize', 12)