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paper_figure_10_fPCA_doseeffect_comprehensivebasis.m
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paper_figure_10_fPCA_doseeffect_comprehensivebasis.m
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%% Paper argumentation for fPCA part (figure 2)
% 0. Cut signals in 2 parts dominated by a) Deterministic rise (t = [50 200]) b) Stochastic oscillations (t = [200 650])
% 1. Do fPCA for all ligands at all doses (no inhibitors) for t = [50 200]
% --> PC2vs3 - IGF one axis - BTC other axis - EGF/HGF/HRG inbetween - EPR/FGF not responding
% Plot first 4 harmonics --> argument for choosing PCs 2 and 3
% 2. Visualize this with ellipses instead of points for IGF and BTC
% The following points are moved to figure 3
% 3. Subtract mean + first 3 harmonics (plot) from data for t = [200 650]
% --> Histograms for no dose + highest dose with threshold
% cell-to-cell heterogeneity <-> time-courses to show oscillations
% Ligands triggering subpopulation to oscillate; Others don't
% 4. Do same analysis for inhibitor data (EGF and HGF): MEKi induces oscillations; AKTi represses oscillations
% (Counter-intuitive: EGF-MEKi population mean like IGF, oscillations however not suppressed as for IGF)
close all
clear all
clc
remotepath = mypath();
fdaMPath = [remotepath 'fda'];
addpath(fdaMPath)
grabdataPath = [remotepath 'Code + Stage and Outputsignal'];
addpath(grabdataPath)
% Get properties of sites by calling siteprop(site)
% All ligands + EGF with Inhibitors
% sites = [1 2 4:10 17:-1:11 24:30 37:-1:31 41 42 44:50 57:-1:51 64:69];
sites_for_harmonics = [4:10 17:-1:11 24:30 37:-1:31 44:50 57:-1:51 64:69];
sites = sites_for_harmonics;
% sites = [1 4];
times = cell(0);
signals = cell(0);
celltype = [];
for isite = sites
if exist(remotepath,'dir')
[timestamp,intensity] = grabdata_new(isite,'Images and Data');
else
load(['./Workspaces/site_' num2str(isite)])
times{end+1} = timestamp;
end
log_trafo = 1; % log-transform signal
if log_trafo
signals{end+1} = log10(intensity);
else
signals{end+1} = intensity;
end
celltype = [celltype ones(1,size(intensity,2))*isite];
end
%timestamp = times{1}; % same time sampling for all data sets
c_signal = cell2mat(signals);
% return
%% Register to mean value in time range
close all
time_range = [50 200];
time_range = [50 510]; % For comprehensive basis
[tmp range_ind_min] = min(abs(timestamp - time_range(1)));
[tmp range_ind_max] = min(abs(timestamp - time_range(2)));
range_ind = range_ind_min:range_ind_max;
time_range_reg = [50 120];
[tmp range_ind_min] = min(abs(timestamp - time_range_reg(1)));
[tmp range_ind_max] = min(abs(timestamp - time_range_reg(2)));
range_ind_reg = range_ind_min:range_ind_max;
figure
posFig = get(gcf,'Position');
% posFig(4) = posFig(4)/2;
set(gcf,'Position',posFig)
set(gcf,'PaperPosition', [0 0 posFig(3) posFig(4)]./10);
site_lig_ind = [];
site_lig_name = {};
site_lig_dose = [];
site_inh_name = {};
site_inh_dose = [];
% Exclude Inhibitor data
for isite = sites_for_harmonics % only plot ligands used for harmonics
s = siteprop(isite);
site_lig_ind = [site_lig_ind s.lig_index];
site_lig_name{end+1} = s.lig_name;
site_lig_dose = [site_lig_dose s.lig_dose];
site_inh_name{end+1} = s.inh_name;
site_inh_dose = [site_inh_dose s.inh_dose];
end
nrows = 7;
ncols = 7;
for iplot = 1:length(sites_for_harmonics)
subplot(nrows,ncols,iplot)
% c_signal(:,celltype == sites_for_harmonics(iplot)) = c_signal(:,celltype == sites_for_harmonics(iplot)) - nanmean(nanmean(c_signal(range_ind_reg,celltype == sites_for_harmonics(iplot))));
plot(repmat(timestamp(range_ind),1,sum(celltype == sites_for_harmonics(iplot))),c_signal(range_ind,celltype == sites_for_harmonics(iplot)),'g','color',[0.7 0.7 0.7])
hold on
plot(timestamp(range_ind),nanmean(c_signal(range_ind,celltype == sites_for_harmonics(iplot)),2),'color','k','LineWidth',2)
title([site_lig_name{iplot} num2str(site_lig_dose(iplot))])
ylim = [-1 1]*.04;
if ~log_trafo
ylim = 10.^ylim;
end
set(gca,'XLim',time_range,'YLim',ylim)
end
% c_signal = c_signal - repmat(nanmean(c_signal(range_ind_reg,:),1),size(c_signal,1),1);
%% Generate spline fits to data-sets given in sites_for_harmonics
% close all
nbasis = 20;
nbasis = 61; % For comprehensive basis
% time_range = [min(timestamp) max(timestamp)];
ind_harm = ismember(celltype,sites_for_harmonics);
ind_fit = ~ind_harm;
basis = create_bspline_basis([timestamp(range_ind(1)) timestamp(range_ind(end))], nbasis);
smoothed_data = smooth_basis(timestamp(range_ind),c_signal(range_ind,ind_harm),basis);
% return
f = figure;
set(f,'DefaultAxesColorOrder',jet(size(c_signal(1,ind_harm),2)))
hold on
plot(smoothed_data)
plot(timestamp(range_ind),c_signal(range_ind,ind_harm),'o')
%% Make FPCA with data generated in previous block
% close all
nharm = 5;
%c_signal_pcastr = pca_fd(smoothed_data, nharm, fdPar(basis, int2Lfd(2), 0));
c_signal_pcastr = pca_fd(smoothed_data, nharm, fdPar(basis, int2Lfd(2), 0), 0); % WITHOUT CENTERING!!
% c_signal_pcastr = varmx_pca(c_signal_pcastr);
% return
% plot_pca_fd(c_signal_pcastr, 1, 0)
% c_signal_rotpcastr = varmx_pca(c_signal_pcastr);
% plot_pca_fd(c_signal_rotpcastr, 1, 0)
%% Figure 2A: fPCA with dose-dependend colored ligand level
close all
% Define principal components to be plotted
pcs = [1 3];
% Unregistered data - Harm 1: DC; Harm 2: Rise; Harm 3: Peak
% angle1 = 20;
% angle2 = 0;
% angle3 = -10;
angle1 = -25;
angle2 = 5;
angle3 = -5;
% Registered data - Harm 1: SS_afterStim; Harm 2: SS_preStim; Harm 3: Peak
% angle1 = 15;
% angle2 = -7;
% Old:
% angle = -10; % rotation angle to right [degree]
% Comprehensive basis
angle1 = 33;
angle2 = -3;
angle3 = 15;
angle4 = 0;
Rmat1 = [cos(2*pi*angle1/360) sin(2*pi*angle1/360) 0; ...
-sin(2*pi*angle1/360) cos(2*pi*angle1/360) 0; ...
0 0 1];
Rmat2 = [cos(2*pi*angle2/360) 0 sin(2*pi*angle2/360); ...
0 1 0; ...
-sin(2*pi*angle2/360) 0 cos(2*pi*angle2/360)];
Rmat3 = [1 0 0; ...
0 cos(2*pi*angle3/360) sin(2*pi*angle3/360); ...
0 -sin(2*pi*angle3/360) cos(2*pi*angle3/360)];
Rmat4 = [cos(2*pi*angle4/360) 0 sin(2*pi*angle4/360); ...
0 1 0; ...
-sin(2*pi*angle4/360) 0 cos(2*pi*angle4/360)];
Rmat = Rmat4 * Rmat3 * Rmat2 * Rmat1;
flipharm = ones(1,nharm);
% Has to be adjusted according to angles
% flipharm(1:4) = [1 1 -1 1]; % Unregistered
flipharm(1:3) = [1 1 -1]; % Unregistered
flipharm(1:3) = [1 1 -1];
unitypes = unique(celltype(ind_harm));
site_lig_ind = [];
site_lig_name = {};
site_lig_dose = [];
site_inh_name = {};
site_inh_dose = [];
% Exclude Inhibitor data
for isite = sites_for_harmonics % only plot ligands used for harmonics
s = siteprop(isite);
site_lig_ind = [site_lig_ind s.lig_index];
site_lig_name{end+1} = s.lig_name;
site_lig_dose = [site_lig_dose s.lig_dose];
site_inh_name{end+1} = s.inh_name;
site_inh_dose = [site_inh_dose s.inh_dose];
end
sites_remain = find(~site_inh_dose);
uni_lig = unique(site_lig_ind(sites_remain));
lig_min = min(site_lig_dose(sites_remain));
lig_max = max(site_lig_dose(sites_remain));
ncolor = 201;
% colmap = flipud(jet(ncolor));
colmap = flipud(winter(ncolor));
color_doses = 10.^linspace(max(log10([lig_min 1])),log10(lig_max),ncolor);
% ligs_to_plot = 1:length(uni_lig); % Plot all
ligs_to_plot = [2 7];
% rowstocols = 0.3;
rowstocols = 0;
nrows = ceil((2*length(ligs_to_plot)+1)^rowstocols);
ncols = ceil((2*length(ligs_to_plot)+1) / nrows);
figure
posFig = get(gcf,'Position');
posFig(4) = posFig(4)/2.5;
% posFig(4) = posFig(4)/3;
set(gcf,'Position',posFig)
set(gcf,'PaperPosition', [0 0 posFig(3) posFig(4)]./20);
flipped_scores = repmat(flipharm,size(c_signal_pcastr.harmscr,1),1).*c_signal_pcastr.harmscr;
STD = 1.5; %# 2 standard deviations
conf = 2*normcdf(STD)-1; %# covers around 95% of population
scale = chi2inv(conf,2); %# inverse chi-squared with dof=#dimensions
for ilig_plot = 1:length(ligs_to_plot)
ilig = ligs_to_plot(ilig_plot);
subplot(nrows,ncols,(2*(ilig_plot-1)+1):(2*ilig_plot))
box on
hold on
tmpind = find(site_lig_ind(sites_remain) == uni_lig(ilig));
title(site_lig_name{sites_remain(tmpind(1))})
x_scores = (Rmat(pcs(1),:) * flipped_scores(:,1:3)')';
y_scores = (Rmat(pcs(2),:) * flipped_scores(:,1:3)')';
plot(x_scores,y_scores,'.','Color',[.7 .7 .7]);
for isite = tmpind
% Colored
[tmp color_ind] = min(abs(color_doses-site_lig_dose(sites_remain(isite))));
mycolor = colmap(color_ind,:);
plot(x_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:),y_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:),'.','Color',mycolor);
%# substract mean
Mu = mean( [x_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:) y_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:)] );
X0 = bsxfun(@minus, [x_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:) y_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:)], Mu);
%# eigen decomposition [sorted by eigen values]
Cov = cov(X0) * scale;
[V D] = eig(Cov);
[D order] = sort(diag(D), 'descend');
D = diag(D);
V = V(:, order);
t = linspace(0,2*pi,100);
e = [cos(t) ; sin(t)]; %# unit circle
VV = V*sqrt(D); %# scale eigenvectors
e = bsxfun(@plus, VV*e, Mu'); %#' project circle back to orig space
%# plot cov and major/minor axes
% plot(e(1,:), e(2,:), 'Color',mycolor);
tmpx = e(1,:);
tmpy = e(2,:);
% ltmp = patch(tmpx, tmpy, ones(size(tmpx)), ones(size(tmpx)));
% set(ltmp, 'FaceColor', mycolor, 'EdgeColor', 'none', 'FaceAlpha', .3);
end
set(gca,'XLim',[min(x_scores) max(x_scores)]*1.1)
aspRatioFig = posFig(3)/posFig(4);
posSubplot = get(gca,'Position');
aspRatioSubplot = posSubplot(3)/posSubplot(4);
% set(gca,'YLim',get(gca,'XLim')/(aspRatioFig*aspRatioSubplot)-.03) % PC1 vs PC3
% set(gca,'YLim',get(gca,'XLim')/(aspRatioFig*aspRatioSubplot)+.03) % PC1 vs PC2
if ilig_plot == 1
ylabel(['PC ' num2str(pcs(2))])
arrow([-.13 -.1],[.2 -.1],'Width',.5,'Length',7)
set(gca,'YTick',-.1:.1:.2)
end
if ilig_plot == length(ligs_to_plot)-1
xlabel(['PC ' num2str(pcs(1))])
% set(gca,'YTickLabel',[])
end
if ilig_plot == length(ligs_to_plot)
% arrow([-.13 .08],[.05 .2],'Width',.5,'Length',7)
arrow([-.13 .06],[.02 .15],'Width',.5,'Length',7)
set(gca,'YTickLabel',[])
end
end
h = get(gca);
subplot(nrows,ncols,2*ilig_plot+1)
clim = log10([lig_min lig_max]);
clim(1) = max([clim(1) 0]);
set(gca,'CLim',clim)
colormap(colmap)
% colorbar('Location','North','XTick',log10([1 2.5 5 10 20 50 100]),'XTickLabel',[0 2.5 5 10 20 50 100]) % Horizontal colorbar
colorbar('Location','West','YTick',log10([1 2.5 5 10 20 50 100]),'YTickLabel',[0 2.5 5 10 20 50 100]) % Vertical colorbar
set(gca,'Visible','off')
text(0,-.05,'Ligand dose\newline[ng/ml]')
%% Plot same as above, but in one figure
% colmap = flipud(hsv(3*ncolor));
% colmap = colmap(1:ncolor,:);
colmap = flipud(jet(ncolor));
color_doses = 10.^linspace(max(log10([lig_min 1])),log10(lig_max),ceil(ncolor./2));
color_doses = [-color_doses(end:-1:2) color_doses];
% ligs_to_plot = 1:length(uni_lig); % Plot all
ligs_to_plot = [2 7];
% rowstocols = 0.3;
rowstocols = 0;
nrows = ceil((length(ligs_to_plot))^rowstocols);
ncols = ceil((length(ligs_to_plot)) / nrows);
figure
posFig = get(gcf,'Position');
posFig(4) = posFig(4)/2;
% posFig(4) = posFig(4)/3;
set(gcf,'Position',posFig)
set(gcf,'PaperPosition', [0 0 posFig(3) posFig(4)]./25);
flipped_scores = repmat(flipharm,size(c_signal_pcastr.harmscr,1),1).*c_signal_pcastr.harmscr;
STD = 1.5; %# 2 standard deviations
conf = 2*normcdf(STD)-1; %# covers around 95% of population
scale = chi2inv(conf,2); %# inverse chi-squared with dof=#dimensions
for ilig_plot = 1:length(ligs_to_plot)
ilig = ligs_to_plot(ilig_plot);
subplot(nrows,ncols,1)
box on
hold on
tmpind = find(site_lig_ind(sites_remain) == uni_lig(ilig));
% title(site_lig_name{sites_remain(tmpind(1))})
x_scores = (Rmat(pcs(1),:) * flipped_scores(:,1:3)')';
y_scores = (Rmat(pcs(2),:) * flipped_scores(:,1:3)')';
if ilig_plot == 1
plot(x_scores,y_scores,'.','Color',[.7 .7 .7]);
end
for isite = tmpind
% Colored
rev_fac = 2*(ilig_plot == 1)-1;
[tmp color_ind] = min(abs(color_doses-rev_fac*site_lig_dose(sites_remain(isite))));
mycolor = colmap(color_ind,:);
plot(x_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:),y_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:),'.','Color',mycolor);
%# substract mean
Mu = mean( [x_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:) y_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:)] );
X0 = bsxfun(@minus, [x_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:) y_scores(celltype(ind_harm) == sites_for_harmonics(sites_remain(isite)),:)], Mu);
%# eigen decomposition [sorted by eigen values]
Cov = cov(X0) * scale;
[V D] = eig(Cov);
[D order] = sort(diag(D), 'descend');
D = diag(D);
V = V(:, order);
t = linspace(0,2*pi,100);
e = [cos(t) ; sin(t)]; %# unit circle
VV = V*sqrt(D); %# scale eigenvectors
e = bsxfun(@plus, VV*e, Mu'); %#' project circle back to orig space
%# plot cov and major/minor axes
% plot(e(1,:), e(2,:), 'Color',mycolor);
tmpx = e(1,:);
tmpy = e(2,:);
% ltmp = patch(tmpx, tmpy, ones(size(tmpx)), ones(size(tmpx)));
% set(ltmp, 'FaceColor', mycolor, 'EdgeColor', 'none', 'FaceAlpha', .3);
end
set(gca,'XLim',[min(x_scores) max(x_scores)]*1.1)
aspRatioFig = posFig(3)/posFig(4);
posSubplot = get(gca,'Position');
aspRatioSubplot = posSubplot(3)/posSubplot(4);
set(gca,'YLim',get(gca,'XLim')/(aspRatioFig*aspRatioSubplot)-.03) % PC1 vs PC3
% set(gca,'YLim',get(gca,'XLim')/(aspRatioFig*aspRatioSubplot)+.03) % PC1 vs PC2
% if ilig_plot == 1
ylabel(['PC ' num2str(pcs(2))])
arrow([-.13 -.1],[.2 -.1],'Width',.5,'Length',7)
set(gca,'YTick',-.1:.1:.2)
% end
% if ilig_plot == length(ligs_to_plot)-1
xlabel(['PC ' num2str(pcs(1))])
% set(gca,'YTickLabel',[])
% end
% if ilig_plot == length(ligs_to_plot)
% arrow([-.13 .08],[.05 .2],'Width',.5,'Length',7)
arrow([-.13 .06],[.02 .15],'Width',.5,'Length',7)
% set(gca,'YTickLabel',[])
% end
end
h = get(gca);
subplot(nrows,ncols,2)
clim = log10([lig_min lig_max]);
clim(1) = max([clim(1) 0]);
set(gca,'CLim',clim)
colormap(colmap)
% colorbar('Location','North','XTick',log10([1 2.5 5 10 20 50 100]),'XTickLabel',[0 2.5 5 10 20 50 100]) % Horizontal colorbar
colorbar('Location','West','YTick',log10([1 10 100]),'YTickLabel',{'BTC','No Stim','IGF'}) % Vertical colorbar
set(gca,'Visible','off')
text(0,-.05,'Ligand dose')
return
%% Plot EGF early vs. late time-points
close all
time_range = [50 510];
[tmp range_ind_min] = min(abs(timestamp - time_range(1)));
[tmp range_ind_max] = min(abs(timestamp - time_range(2)));
range_ind = range_ind_min:range_ind_max;
f = figure;
posFig = get(gcf,'Position');
posFig(4) = posFig(4)/1.5;
set(gcf,'Position',posFig)
set(gcf,'PaperPosition', [0 0 posFig(3) posFig(4)]./17);
nrows = 3;
ncols = 5;
subplot(nrows,ncols,[1 2 3 6 7 8 11 12 13])
site_lig_ind = [];
site_lig_name = {};
site_lig_dose = [];
site_inh_name = {};
site_inh_dose = [];
% Exclude Inhibitor data
for isite = sites_for_harmonics % only plot ligands used for harmonics
s = siteprop(isite);
site_lig_ind = [site_lig_ind s.lig_index];
site_lig_name{end+1} = s.lig_name;
site_lig_dose = [site_lig_dose s.lig_dose];
site_inh_name{end+1} = s.inh_name;
site_inh_dose = [site_inh_dose s.inh_dose];
end
iplot = 1; % EGF high dose
first_n = 15; % Plot first_n traces colored
set(f,'DefaultAxesColorOrder',lines(first_n))
plotsignals = find(celltype == sites_for_harmonics(iplot));
plot(repmat(timestamp(range_ind),1,length(plotsignals)),c_signal(range_ind,plotsignals),'g','color',[0.7 0.7 0.7])
hold on
plot(repmat(timestamp(range_ind),1,first_n),c_signal(range_ind,plotsignals(1:first_n)))
plot(timestamp(range_ind),nanmean(c_signal(range_ind,plotsignals),2),'color','k','LineWidth',2)
title([site_lig_name{iplot} num2str(site_lig_dose(iplot)) ' [ng/ml]'])
xlabel('time [min]')
ylabel('log_{10} FOXO3a Cyt/Nuc ratio');
ylim = [-1 1]*.04;
if ~log_trafo
ylim = 10.^ylim;
end
plot([200 200],ylim,'k--')
text(75,.035,'early response\newline(deterministic)')
text(300,.035,'late response\newline(stochastic)')
set(gca,'XLim',time_range,'YLim',ylim)
set(gca,'XTick',50:50:500)
% Figure 2B: Eigenfunctions (new - rotated)
pcs = 1:3;
% rowstocols = 1;
% nrows = ceil(nharm^rowstocols);
% ncols = ceil(nharm / nrows);
time_range = [50 200];
[tmp range_ind_min] = min(abs(timestamp - time_range(1)));
[tmp range_ind_max] = min(abs(timestamp - time_range(2)));
range_ind = range_ind_min:range_ind_max;
times_fine = linspace(timestamp(range_ind(1)),timestamp(range_ind(end)),501);
harm_eval = repmat(flipharm(1:nharm),length(times_fine),1) .* eval_fd(c_signal_pcastr.harmfd,times_fine);
harm_eval_rescale = 2 * repmat(sqrt(c_signal_pcastr.values(1:nharm))',length(times_fine),1) .* harm_eval;
% <-- Why does Ramsay do that?? Destroys normalization and may not be done if harmonics are rotated!
harm_eval_rescale = harm_eval;
% posFig = get(gcf,'Position');
% posFig(3) = posFig(3)/2.5;
% set(gcf,'Position',posFig)
% set(gcf,'PaperPosition', [0 0 posFig(3) posFig(4)]./20);
harmscr = (Rmat * flipped_scores(:,1:3)')';
propvar = squeeze(sum(harmscr.^2));
propvar = propvar./sum(propvar);
propvar = propvar.*sum(c_signal_pcastr.varprop(1:3));
for iplot = 1:nharm
subplot(nrows,ncols,ncols*(iplot-1)+ncols-1)
if iplot <= length(pcs)
tmpplot = sum(repmat(Rmat(iplot,:),size(harm_eval_rescale,1),1) .* harm_eval_rescale(:,pcs),2);
varper = propvar(iplot);
else
tmpplot = harm_eval_rescale(:,iplot);
varper = c_signal_pcastr.varprop(iplot);
end
plot(times_fine,tmpplot)
title(['Harmonic ' num2str(iplot)])
set(gca,'XLim',time_range)
set(gca,'YLim',[min(min(harm_eval_rescale)) max(max(harm_eval_rescale))]*1.2)
hold on
plot(time_range,[0 0],'--')
% title(['Variance explained: ' num2str(varper*100,3) '%'])
if iplot == nharm
% xlabel('time [min]')
set(gca,'XTick',50:50:200)
else
set(gca,'XTick',[])
end
set(gca,'YTick',[])
end
load('harm_basis.mat') % Contains only harm_basis from all data-sets
time_range = [200 510];
[tmp range_ind_min] = min(abs(timestamp - time_range(1)));
[tmp range_ind_max] = min(abs(timestamp - time_range(2)));
range_ind = range_ind_min:range_ind_max;
times_fine = linspace(timestamp(range_ind(1)),timestamp(range_ind(end)),501);
basis_eval = eval_basis(harm_basis,times_fine);
for iplot = 1:size(basis_eval,2)
subplot(nrows,ncols,ncols*(iplot-1)+ncols)
tmpplot = basis_eval(:,iplot);
plot(times_fine,tmpplot)
title(['Harmonic ' num2str(iplot)])
set(gca,'XLim',time_range)
set(gca,'YLim',[min(min(basis_eval)) max(max(basis_eval))]*1.2)
hold on
plot(time_range,[0 0],'--')
% title(['Variance explained: ' num2str(varper*100,3) '%'])
if iplot == nharm
% xlabel('time [min]')
set(gca,'XTick',200:100:500)
else
set(gca,'XTick',[])
end
set(gca,'YTick',[])
end
%% Figure 2B: Eigenfunctions (new - rotated)
close all
pcs = 1:3;
angle1 = -25;
angle2 = 5;
angle3 = -5;
% Comprehensive basis
angle1 = 10;
angle2 = 0;
angle3 = 20;
% Following works OK and generates 20140130T145713_basis_after_rot.pdf
% flipharm(1:3) = [1 1 -1];
% angle1 = 15;
% angle2 = 60;
% angle3 = 20;
%
% angle4 = -60;
%
% Rmat1 = [cos(2*pi*angle1/360) sin(2*pi*angle1/360) 0; ...
% -sin(2*pi*angle1/360) cos(2*pi*angle1/360) 0; ...
% 0 0 1];
%
% Rmat2 = [cos(2*pi*angle2/360) 0 sin(2*pi*angle2/360); ...
% 0 1 0; ...
% -sin(2*pi*angle2/360) 0 cos(2*pi*angle2/360)];
%
% Rmat3 = [1 0 0; ...
% 0 cos(2*pi*angle3/360) sin(2*pi*angle3/360); ...
% 0 -sin(2*pi*angle3/360) cos(2*pi*angle3/360)];
%
% Rmat4 = [cos(2*pi*angle4/360) 0 sin(2*pi*angle4/360); ...
% 0 1 0; ...
% -sin(2*pi*angle4/360) 0 cos(2*pi*angle4/360)];
%
% Rmat = Rmat4 * Rmat3 * Rmat2 * Rmat1;
% Following works just as the one above but with 3 angles --> 20140130T151326_basis_after_rot_3anglesa.pdf
% flipharm(1:3) = [1 1 -1];
% angle1 = 33;
% angle2 = -3;
% angle3 = 15;
flipharm(1:5) = [1 1 -1 1 1];
angle1 = 33;
angle2 = -3;
angle3 = 15;
angle4 = 0;
Rmat1 = [cos(2*pi*angle1/360) sin(2*pi*angle1/360) 0; ...
-sin(2*pi*angle1/360) cos(2*pi*angle1/360) 0; ...
0 0 1];
Rmat2 = [cos(2*pi*angle2/360) 0 sin(2*pi*angle2/360); ...
0 1 0; ...
-sin(2*pi*angle2/360) 0 cos(2*pi*angle2/360)];
Rmat3 = [1 0 0; ...
0 cos(2*pi*angle3/360) sin(2*pi*angle3/360); ...
0 -sin(2*pi*angle3/360) cos(2*pi*angle3/360)];
Rmat4 = [cos(2*pi*angle4/360) 0 sin(2*pi*angle4/360); ...
0 1 0; ...
-sin(2*pi*angle4/360) 0 cos(2*pi*angle4/360)];
Rmat = Rmat4 * Rmat3 * Rmat2 * Rmat1;
rowstocols = 1;
nrows = ceil(nharm^rowstocols);
ncols = ceil(nharm / nrows);
[tmp range_ind_min] = min(abs(timestamp - time_range(1)));
[tmp range_ind_max] = min(abs(timestamp - time_range(2)));
range_ind = range_ind_min:range_ind_max;
times_fine = linspace(timestamp(range_ind(1)),timestamp(range_ind(end)),501);
harm_eval = repmat(flipharm(1:nharm),length(times_fine),1) .* eval_fd(c_signal_pcastr.harmfd,times_fine);
harm_eval_rescale = harm_eval;
f3 = figure;
hold on
xfac = .4;
yfac = 1;
fontsize = 8;
setFigure(f3,xfac,yfac,fontsize)
harmscr = (Rmat * flipped_scores(:,1:3)')';
propvar = squeeze(sum(harmscr.^2));
propvar = propvar./sum(propvar);
propvar = propvar.*sum(c_signal_pcastr.varprop(1:3));
for iplot = 1:nharm
subplot(nrows,ncols,iplot)
if iplot <= length(pcs)
tmpplot = sum(repmat(Rmat(iplot,:),size(harm_eval_rescale,1),1) .* harm_eval_rescale(:,pcs),2);
varper = propvar(iplot);
else
tmpplot = harm_eval_rescale(:,iplot);
varper = c_signal_pcastr.varprop(iplot);
end
plot(times_fine,tmpplot)
xlabel(['Harmonic ' num2str(iplot)])
set(gca,'XLim',time_range)
% set(gca,'XLim',[50 200])
% set(gca,'YLim',[min(min(harm_eval_rescale)) max(max(harm_eval_rescale))]*1.2)
hold on
plot(time_range,[0 0],'--')
title(['Variance explained: ' num2str(varper*100,3) '%'])
end