%------------------------------------------------------------------------------------------
%
% Title: Calcium Signals in Small Structures
% Filename: XDiffKOn_MergedAtomics.m
% Author: Ronald van Elburg
%
% Associated Paper:
% Cornelisse LN, van Elburg RAJ, Meredith RM, Yuste R, Mansvelder HD (2007)
% High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines:
% Consequences for Spine Calcium Kinetics and Buffer Capacity.
% PLoS ONE 2(10): e1073 doi:10.1371/journal.pone.0001073
%------------------------------------------------------------------------------------------
% close all
clear all
addpath(genpath('.'))
FontWeight='bold';
FontWeightColorBar='normal';
addpath(genpath('.'))
location_colorbar='East';
colorbarinplot=0;
x_spine=0.45;
y_spine=1;
x_dendrite=0.45;
y_dendrite=1;
XTick=0.25:0.25:0.75;
YTick=0:0.5:2;
RiseColorBarTicks=2:1.5:8;
RiseColorBarTickLabels={'2','','5','','8'};
DecayColorBarTicks=0:100:400;
DecayColorBarTickLabels={' 0','','200','','400'}
f1=openfig('..\Output\CSEXDiffKOnD__CombinedContours_Dye_KPlus_Dye_Plot.fig');
axeshandle2=gca;
f2=openfig('..\Output\CSEXDiffKOnS__CombinedContours_Dye_KPlus_Dye_Plot.fig');
axeshandle3=gca;
f3=openfig('..\Output\CSEXDiffKOnD__DecayTimes_Dye_KPlus_Dye_Plot.fig');
axeshandle4=gca;
f4=openfig('..\Output\CSEXDiffKOnS__DecayTimes_Dye_KPlus_Dye_Plot.fig');
axeshandle5=gca;
f5=openfig('..\Output\CSEXDiffKOnD__RiseTimes_Dye_KPlus_Dye_Plot.fig');
axeshandle6=gca;
f6=openfig('..\Output\CSEXDiffKOnS__RiseTimes_Dye_KPlus_Dye_Plot.fig');
axeshandle7=gca;
axes_handles=zeros(3,2);
bar_handles=zeros(3,2);
%%
figure(600)
axeshandle1=subplot(2,3,6);
axes_handles(3,2)=axeshandle2;
swapfigures(axeshandle1,axeshandle2)
axes(axeshandle2)
plot(axeshandle2,x_dendrite,y_dendrite,'b+','MarkerSize',6)
% text(.4,9000,'\fontsize{16}\bfF')
% image(1:20,1:20,magic(20))
% bar_handles(3,2)=colorbar('peer',axeshandle2,location_colorbar)
set(axeshandle2,'LineWidth','default')
axeshandle1=subplot(2,3,3);
axes_handles(3,1)=axeshandle3;
swapfigures(axeshandle1,axeshandle3)
axes(axeshandle3)
plot(axeshandle3,x_spine,y_spine,'r+','MarkerSize',6)
% text(.4,9000,'\fontsize{16}\bfC')
% bar_handles(3,1)=colorbar('peer',axeshandle3,location_colorbar)
set(axeshandle3,'LineWidth','default')
axeshandle1=subplot(2,3,5);
axes_handles(2,2)=axeshandle4;
swapfigures(axeshandle1,axeshandle4)
bar_handles(2,2)=colorbar('peer',axeshandle4,location_colorbar,'XColor','k','YColor','k');
axes(axeshandle4)
caxis([0 400])
bar_handles(2,2)=colorbar('peer',axeshandle4,location_colorbar,'XColor','k','YColor','k','FontWeight',FontWeightColorBar,'YLim',[0 400],'YTick',DecayColorBarTicks,'YTickLabel',DecayColorBarTickLabels);
plot(axeshandle4,x_dendrite,y_dendrite,'b+','MarkerSize',6)
% text(.4,9000,'\color{white}\bf\fontsize{16}E')
set(get(axeshandle4,'Xlabel'),'String', 'K_{on,dye} (ms^{-1} \muM^{-1})','FontWeight',FontWeight)
set(axeshandle4,'YAxisLocation','right')
axeshandle1=subplot(2,3,2);
axes_handles(2,1)=axeshandle5;
swapfigures(axeshandle1,axeshandle5)
axes(axeshandle5)
caxis([0 400])
bar_handles(2,1)=colorbar('peer',axeshandle5,location_colorbar,'XColor','k','YColor','k','FontWeight',FontWeightColorBar,'YLim',[0 400],'YTick',DecayColorBarTicks,'YTickLabel',DecayColorBarTickLabels);
plot(axeshandle5,x_spine,y_spine,'r+','MarkerSize',6)
% text(.4,9000,'\color{white}\bf\fontsize{16}B')
set(axeshandle5,'YAxisLocation','right')
axeshandle1=subplot(2,3,4);
axes_handles(1,2)=axeshandle6;
swapfigures(axeshandle1,axeshandle6)
axes(axeshandle6)
caxis([2 8])
bar_handles(1,2)=colorbar('peer',axeshandle6,location_colorbar,'XColor','k','YColor','k','FontWeight',FontWeightColorBar,'YLim',[2 8],'YTick',RiseColorBarTicks,'YTickLabel',RiseColorBarTickLabels);
plot(axeshandle6,x_dendrite,y_dendrite,'b+','MarkerSize',6)
% text(.4,9000,'\color{white}\bf\fontsize{16}D')
set(get(axeshandle6,'Ylabel'),'String', 'Diffusion factor (1)','FontWeight',FontWeight)
% set(get(axeshandle6,'Xlabel'),'String', 'Extrusion rate (\mum ms^{-1})')
axeshandle1=subplot(2,3,1);
axes_handles(1,1)=axeshandle7;
swapfigures(axeshandle1,axeshandle7)
axes(axeshandle7)
caxis([2 8])
bar_handles(1,1)=colorbar('peer',axeshandle7,location_colorbar,'XColor','k','YColor','k','FontWeight',FontWeightColorBar,'YLim',[2 8],'YTick',RiseColorBarTicks,'YTickLabel',RiseColorBarTickLabels);
plot(axeshandle7,x_spine,y_spine,'r+','MarkerSize',6)
% text(.4,9000,'\color{white}\bf\fontsize{16}A')
set(get(axeshandle7,'Ylabel'),'String', 'Diffusion factor (1)','FontWeight',FontWeight)
close([f1,f2,f3,f4,f5,f6])
%%
% title(axes_handles(2,1),'Influence calcium binding characteristics on fluoresence rise and decay time','Fontsize',12,'HorizontalAlignment','center')
set(axes_handles,'FontSize',9,'FontWeight',FontWeight,'XTick',XTick,'YTick',YTick,'TickDir','out')
RedistributeSubplots(axes_handles,3,2,0.1,0.1)
set(axes_handles,'TickDir','out')
%% -----------------------Set contour lines to correct color
x_plot_size=3;
y_plot_size=2;
for y_coord=1:1:y_plot_size
for x_coord=1:1:x_plot_size
children=findobj(axes_handles(x_coord,y_coord),'Type','hggroup');
for child=children
set(child,'LineWidth',3)
if(y_coord==1)
set(child,'LineColor','r')
else
set(child,'LineColor','b')
end
end
end
end
%% ------------------------- Remove unneeded colorbars ------------------------------------
colorbarShrink=0.8;
for y_coord=1:1:y_plot_size
for x_coord=1:1:x_plot_size
if(colorbarinplot==1)
if(x_coord==3)
set(bar_handles(x_coord,y_coord),'Visible','Off')
else
set(bar_handles(x_coord,y_coord),'Visible','On')
pos=get(axes_handles(x_coord,y_coord),'Position');
pos2=get(bar_handles(x_coord,y_coord),'Position');
pos2=[pos(1)+pos(3)-1.5*pos2(3),pos(2)+pos(4)*(0.95-colorbarShrink),pos2(3),pos(4)*colorbarShrink];
set(bar_handles(x_coord,y_coord),'Position',pos2)
end
else %colorbarinplot~=1
pos=get(axes_handles(x_coord,y_coord),'Position');
if(x_coord==3)
set(axes_handles(x_coord,y_coord),'Position',pos+[0.06,0,0,0]);
elseif(x_coord==2)
set(axes_handles(x_coord,y_coord),'Position',pos+[0.06,0,0,0]);
else
set(axes_handles(x_coord,y_coord),'Position',pos+[-0.02,0,0,0]);
end
if(x_coord==3)
set(bar_handles(x_coord,y_coord),'Visible','Off')
else
set(bar_handles(x_coord,y_coord),'Visible','On')
end
end
end
end
%%
%set(bar_handles,'FontWeight',FontWeightColorBar)
if(colorbarinplot~=1)
for y_coord=1:1:y_plot_size
pos1=get(axes_handles(1,y_coord),'Position');
pos2=get(axes_handles(2,y_coord),'Position');
barpos1=get(bar_handles(1,y_coord),'Position');
% barpos2=get(bar_handles(2,y_coord),'Position');
barpos1=[(pos1(1)+pos1(3)+pos2(1)-barpos1(3))/2,pos1(2)+pos1(4)*(1-colorbarShrink),barpos1(3),pos1(4)*colorbarShrink];
set(bar_handles(1,y_coord),'Position',barpos1,'YAxisLocation','left','FontWeight',FontWeightColorBar)
barpos2=[(pos1(1)+pos1(3)+pos2(1)-barpos1(3))/2,pos1(2)+pos1(4)*(1-colorbarShrink),barpos1(3),pos1(4)*colorbarShrink];
set(bar_handles(2,y_coord),'Position',barpos2,'YAxisLocation','right','FontWeight',FontWeightColorBar)
end
end
%%
orient landscape
set(gcf,'PaperType','A4')
saveas(gcf, '..\Output\XDiffKOn_CombinedFigures','fig')
saveas(gcf, '..\Output\XDiffKOn_CombinedFigures','png')
saveas(gcf, '..\Output\XDiffKOn_CombinedFigures','pdf')