off-motion-receptive-fields/receptiveFields/plotRFsAlignedWithFit.m

function plotRFsAlignedWithFit(StimTableCell, rSqThresh, respIndThresh, figDir, nameSuffix, varargin)
if nargin > 5
    alignAll = varargin{1};
else
    alignAll = false;
end
% [tcArrayCell, responseIndArrayCell, rSquareArrayCell, fitParamsCell, ...
%  tcExtCellArray, tcArgExtCellArray] = cellfun(@getTuningCurveArrayFromTable, ...
%                                               StimTableCell, 'uni', 0);
 [tcArrayCell, responseIndArrayCell, rSquareArrayCell, fitParamsCell, ...
  flyIndsCell, tcExtCellArray, tcArgExtCellArray] = getStimArraysForSameRois(StimTableCell);                                          
% Align to fit
posCell = cellfun(@(x) arrayfun(@(y) y.b1, x, 'uni', 0), fitParamsCell, 'uni', 1);
widthCell = cellfun(@(x) arrayfun(@(y) 2 * (2 * sqrt(log(2))) * y.c1, x, 'uni', 0), ...
                    fitParamsCell, 'uni', 1); % The 2 factor is because of bar separation.

lagsCell = cellfun(@(x, y) round(x - size(y, 2) / 2), posCell, tcArrayCell, 'uni', 0);
barRFs = cellfun(@(x, y) alignRFsToAbsMax(x, 0, y'), tcArrayCell, lagsCell, 'uni', 0);
validIndsCell = cellfun(@(x, y) x(:) > rSqThresh & y(:) > respIndThresh, ...
                        rSquareArrayCell, responseIndArrayCell, 'uni', 0)';
%% Blank epoch was already deleted, now delete vertical bars on edges of screen.
barRFs{2}(:, end-1: end) = [];
barRFs{4}(:, end-1: end) = [];
barRFs{2}(:, 1: 2) = [];
barRFs{4}(:, 1: 2) = [];
%%
if alignAll
    validAll = validIndsCell{1} & validIndsCell{2} & ...
               validIndsCell{3} & validIndsCell{4};
    offX = barRFs{1}(validAll, :);
    offY = barRFs{2}(validAll, :);
    onX = barRFs{3}(validAll, :);
    onY = barRFs{4}(validAll, :);
else
    offX = barRFs{1}(validIndsCell{1}&validIndsCell{2}, :);
    offY = barRFs{2}(validIndsCell{2}&validIndsCell{1}, :);
    onX = barRFs{3}(validIndsCell{3}&validIndsCell{4}, :);
    onY = barRFs{4}(validIndsCell{4}&validIndsCell{3}, :);
end

% normalize to peak and smooth and normalize again.
maxNorm = @(x, dim) x ./ max(abs(x), [], dim);
getRow = @(x, nRow) x(nRow, :);
normRFs = cellfun(@(x) cell2mat(arrayfun(@(y) smooth(getRow(maxNorm(x,2), y))', 1: size(x, 1), 'uni', 0)'), ...
                  {offX, offY, onX, onY}, 'uni', 0);
normRFs = cellfun(@(x) maxNorm(x,2), normRFs, 'uni', 0);
%%
% Plot lasagna plots, separate figures for off and on, and reapeated panel
% is to have a colorbar that does not distort existing axis of interest.
plotLasagnaRFs(offX, offY, 'OFF')
plotLasagnaRFs(onX, onY, 'ON')

function plotLasagnaRFs(xRFs, yRFs, polarityStr)
%% Plot traces and average above colormap of single cell responses
% Last subplot is a dummy to avoid resizing when colorbar is used.
hFig = createPrintFig(15 * [ 1 2/3]);
hSubAx = plotLasagnaTracesFromCell(gcf, {xRFs, yRFs, xRFs}, brewermap(6, 'Paired'));
colorbar;
arrayfun(@prettifyAxes, hSubAx);
arrayfun(@offsetAxes, hSubAx);
figFileName = ['RFcurves-' polarityStr '-XY-lasagna-' nameSuffix];    
print(hFig, [figDir figFileName '.pdf'], '-dpdf');

end

end