%This script file checks to see what graphs the user wants and then subplots the graphs 
%accordingly so that the space on the screen is maximized for efficiency

if (strcmp(get(gxlin,'Checked'),'on') | strcmp(get(gylin,'Checked'),'on') | strcmp(get(grlin,'Checked'),'on')) & (strcmp(get(gxlog,'Checked'),'on') | strcmp(get(gylog,'Checked'),'on') | strcmp(get(grlog,'Checked'),'on'))


	subplot(2,1,1);
	if strcmp(get(gxlin,'Checked'),'on'),
		plot(tau,X,'b'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			plot(tau1Xplot,linex1,'c',tau2Xplot,linex2,'c'),hold on;
			plot(fitTimeX,X(fitTimeX/.01),'b*',critpointX*.01,X(critpointX),'cx'), hold on;
		end
	end
	if strcmp(get(gylin,'Checked'),'on'),
		plot(tau, Y, 'y'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			plot(tau1Yplot,liney1,'g',tau2Yplot,liney2,'g'), hold on;
			plot(fitTimeY,Y(fitTimeY/.01),'yo',critpointY*.01,Y(critpointY),'gx'), hold on;
		end
	end
  	if strcmp(get(grlin,'Checked'),'on'),
		plot(tau, R, 'r'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			plot(tau1Rplot,liner1,'m',tau2Rplot,liner2,'m'), hold on;
			plot(fitTimeR,R(fitTimeR/.01),'r*',critpointR*.01,R(critpointR),'mx'), hold on;
		end
	end
	title('Linear Stabilogram-Diffusion plot')
	text(8.5,10,'X','color','b');
	text(9,10,'Y','color','y');
	text(9.5,10,'R','color','r');
	axis([0 10 0 max(R)+10]);
	
%Plot loglog graphs
	subplot(2,1,2);
	if strcmp(get(gxlog,'Checked'),'on'),
		loglog(tau,X,'b'),hold on;
		if strcmp(get(greg,'Checked'),'on'),
			loglog(tau1Xplot,linex1log,'c',tau2Xplot,linex2log,'c'),hold on;
			loglog(fitTimeX,X(fitTimeX/.01),'b*',critpointX*.01,X(critpointX),'cx'), hold on;
		end
	end
	if strcmp(get(gylog,'Checked'),'on'),
		loglog(tau, Y, 'y'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			loglog(tau1Yplot,liney1log,'g',tau2Yplot,liney2log,'g'),hold on;
			loglog(fitTimeY,Y(fitTimeY/.01),'yo',critpointY*.01,Y(critpointY),'gx'), hold on;
		end
	end
	if strcmp(get(grlog,'Checked'),'on'),
		loglog(tau, R, 'r'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			loglog(tau1Rplot,liner1log,'m',tau2Rplot,liner2log,'m'), hold on;
			loglog(fitTimeR,R(fitTimeR/.01),'r*',critpointR*.01,R(critpointR),'mx'), hold on;
		end
	end
	axis([.01 10 .1 150]);
	xlabel('time interval (s)');
	zoom on
	title('Log-log Stabilogram-Diffusion plot')
	text(3,.2,'X','color','b');
	text(5,.2,'Y','color','y');
	text(7,.2,'R','color','r');

elseif (strcmp(get(gxlin,'Checked'),'on') | strcmp(get(gylin,'Checked'),'on') | strcmp(get(grlin,'Checked'),'on')) | (strcmp(get(gxlog,'Checked'),'on') | strcmp(get(gylog,'Checked'),'on') | strcmp(get(grlog,'Checked'),'on'))

	if strcmp(get(gxlin,'Checked'),'on'),
		title('Linear Stabilogram-Diffusion plot')
		text(8.5,5,'X','color','b');
		text(9,5,'Y','color','y');
		text(9.5,5,'R','color','r');
		plot(tau,X,'b'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			plot(tau1Xplot,linex1,'c',tau2Xplot,linex2,'c'),hold on;
			plot(fitTimeX,X(fitTimeX/.01),'b*',critpointX*.01,X(critpointX),'cx'), hold on;
		end
	end
	if strcmp(get(gylin,'Checked'),'on'),
		title('Linear Stabilogram-Diffusion plot')
		text(8.5,5,'X','color','b');
		text(9,5,'Y','color','y');
		text(9.5,5,'R','color','r');
		plot(tau, Y, 'y'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			plot(tau1Yplot,liney1,'g',tau2Yplot,liney2,'g'), hold on;
			plot(fitTimeY,Y(fitTimeY/.01),'yo',critpointY*.01,Y(critpointY),'gx'),hold on;
		end
	end
  	if strcmp(get(grlin,'Checked'),'on'),
		title('Linear Stabilogram-Diffusion plot')
		text(8.5,5,'X','color','b');
		text(9,5,'Y','color','y');
		text(9.5,5,'R','color','r');
		plot(tau, R, 'r'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			plot(tau1Rplot,liner1,'m',tau2Rplot,liner2,'m'), hold on;
			plot(fitTimeR,R(fitTimeR/.01),'r*',critpointR*.01,R(critpointR),'mx'), hold on;
		end
	end
	
%Plot loglog graphs
	if strcmp(get(gxlog,'Checked'),'on'),
		title('Log-log Stabilogram-Diffusion plot')
		axis([.01 10 .1 150]);
		text(3,.2,'X','color','b');
		text(5,.2,'Y','color','y');
		text(7,.2,'R','color','r');
		loglog(tau,X,'b'),hold on;
		if strcmp(get(greg,'Checked'),'on'),
			loglog(tau1Xplot,linex1log,'c',tau2Xplot,linex2log,'c'),hold on;
			loglog(fitTimeX,X(fitTimeX/.01),'b*',critpointX*.01,X(critpointX),'cx'), hold on;
		end
	end
	if strcmp(get(gylog,'Checked'),'on'),
		title('Log-log Stabilogram-Diffusion plot')
		axis([.01 10 .1 150]);
		text(3,.2,'X','color','b');
		text(5,.2,'Y','color','y');
		text(7,.2,'R','color','r');
		loglog(tau, Y, 'y'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			loglog(tau1Yplot,liney1log,'g',tau2Yplot,liney2log,'g'),hold on;
			loglog(fitTimeY,Y(fitTimeY/.01),'yo',critpointY*.01,Y(critpointY),'gx'), hold on;
		end
	end
	if strcmp(get(grlog,'Checked'),'on'),
		title('Log-log Stabilogram-Diffusion plot')
		axis([.01 10 .1 150]);
		text(3,.2,'X','color','b');
		text(5,.2,'Y','color','y');
		text(7,.2,'R','color','r');
		loglog(tau, R, 'r'), hold on;
		if strcmp(get(greg,'Checked'),'on'),
			loglog(tau1Rplot,liner1log,'m',tau2Rplot,liner2log,'m'), hold on;
			loglog(fitTimeR,R(fitTimeR/.01),'r*',critpointR*.01,R(critpointR),'mx'), hold on;
		end
	end
	
	zoom on
	xlabel('time interval (s)');
end