\setupcode{ importTool('GPmat') gpmatToolboxes randn('seed', 1e4); rand('seed', 1e4); lineWidth = 4; textWidth = 13; colWidth = 5; markerSize = 2; markerWidth = 4; markerType = 'kx';
redColor = [1, 0, 0]; greenColor = [0, 1, 0]; blueColor = [0, 0, 1]; magentaColor = [1, 0, 1]; blackColor = [0, 0, 0]; fillColor = [0.7 0.7 0.7]; negative = false; if blackBackground negative = true; redColor = 1-redColor; greenColor = 1-greenColor; blueColor = 1-blueColor; magentaColor = 1-magentaColor; blackColor = 1- blackColor; fillColor = 1-fillColor; end directory = '\writeDiagramsDir/sysbio/'; }
ODE1 ARTIFICIAL EXAMPLE
\code{ load ../../../gpsim/matlab/demToyProblem7.mat
predt = [linspace(0, 18, 100)]'; figure(1), clf order = [4 3 2]; lin1 = []; colors = {blueColor, greenColor, redColor}; hold on; for i = 1:length(order) lin1 = [lin1; plot(t, truey(:, order(i)-1), 'color', colors{i})]; end set(gca, 'ylim', [0 8]); xlim = get(gca, 'xlim'); ylim = get(gca, 'ylim') line([xlim(1) xlim(1)], ylim, 'color', blackColor) line(xlim, [ylim(1) ylim(1)], 'color', blackColor)
hold on lin2 = []; counter = 0; presentOrder = 0; for i = order presentOrder = presentOrder + 1; for j = 1:length(model.timesCell{i}) counter = counter + 1; indices(counter, 1) = i; indices(counter, 2) = j; indices(counter, 3) = presentOrder; end end ind = [1]; tvals = cell(length(model.timesCell)); includeText = []; for i = 1:size(indices, 1) offset = 0; for j = 1:indices(i, 1)-1 offset = offset + length(model.timesCell{j}); end ind = [ind indices(i, 2)+offset]; tvals{indices(i, 1)} = [tvals{indices(i, 1)}; model.timesCell{indices(i, 1)}(indices(i, ... 2))];
proteinKern = model.kern.comp{1};
K = rbfKernCompute(proteinKern, 0, predt);
counter = 0;
for j=order
counter = counter + 1;
if ~isempty(tvals{j})
K = [K; real(simXrbfKernCompute(model.kern.comp{j}, proteinKern, ...
tvals{j}, predt))];
end
end
invK = pdinv(model.K(ind, ind));
obsY = model.m(ind, 1);
predF = K'invKobsY;
varF = kernDiagCompute(proteinKern, predt) - sum(K.(invKK), 1)';
figure(1) lin2 = [ plot(model.timesCell{indices(i, 1)}(indices(i, 2)), ... [repmat(NaN, 1, indices(i, 3)-1) model.y(ind(end) - 1)], 'x', ... 'color', colors{indices(i, 3)})]; set(lin1, 'lineWidth', 2); set(lin1, 'markersize', 10); set(lin2, 'lineWidth', 4); set(lin2, 'markersize', 10); %set(gca, 'fontname', 'arial', 'fontsize', 24, 'xlim', xlim, 'ylim', [0 8]) fileName = ['toyGeneData' num2str(i)]; printLatexPlot(fileName, directory, 0.4*textWidth); includeText = [includeText '###\n\n'] includeText = [includeText '\includeimg{' directory fileName '}{45%}{}{left}'];
figure(2), clf
hold on
stdVals = sqrt(varF);
fillColor = [0.7 0.7 0.7];
patch([predt; predt(end:-1:1)], ...
[predF; predF(end:-1:1)] ...
+ 2*[stdVals; -stdVals(end:-1:1)], ...
fillColor,'edgecolor',fillColor)
% fill(, ...
% fillColor,'EdgeColor',fillColor)
lin = plot(t, truef, '-', 'color', blueColor);
lin = [lin plot(predt, predF, '-', 'color', blackColor)];
set(lin, 'lineWidth', 4);
set(lin, 'markersize', 10);
%set(gca, 'fontname', 'arial', 'fontsize', 24, 'xlim', xlim)
ylim = [-2 4];
xlim = get(gca, 'xlim');
set(gca, 'ylim', ylim)
line([xlim(1) xlim(1)], ylim, 'color', blackColor)
line(xlim, [ylim(1) ylim(1)], 'color', blackColor)
fileName = ['groundTruthTFData' num2str(i)];
printLatexPlot(fileName, directory, 0.4*textWidth);
includeText = [includeText '\includeimg{' directory fileName '}{45%}{}{right}'];
end
printLatexText(includeText, 'infer-tf-from-gene-text.md', directory)
}
include{\diagramsDir/sysbio/infer-tf-from-gene-text.md}