%Plot CDOM absorption and calculate CDOM absorption over PAR (400-700 nm) and
%at LISST 670 nm

%September 29, 2015 KAF

clear all
%YR150824 
%YR150824=xlsread('/Users/kelsey/Desktop/Dissertation/Profiler Surveys/York River/Axial Surveys/YR150824/CDOM Absorbtion/YR150824_CDOM.xlsx','absorption');
YR150824=xlsread('/Users/kelsey/Desktop/Dissertation/Profiler Surveys/York River/Axial Surveys/YR150824/CDOM Absorbtion/YR150824_CDOM.xlsx','absorption_avg');
YR150824_PAR=YR150824((find(YR150824(:,1)>=400 & YR150824(:,1)<=700)),:);


%YR150827
%YR150827=xlsread('/Users/kelsey/Desktop/Dissertation/Profiler Surveys/York River/Axial Surveys/YR150827/CDOM Absorption/YR150827_CDOM.xlsx','absorption');
YR150827=xlsread('/Users/kelsey/Desktop/Dissertation/Profiler Surveys/York River/Axial Surveys/YR150827/CDOM Absorption/YR150827_CDOM.xlsx','absorption_avg');
YR150827_PAR=YR150827((find(YR150827(:,1)>=400 & YR150827(:,1)<=700)),:);

figure (1)
plot(YR150824_PAR(:,1),YR150824_PAR(:,2:2:end),'o-','Markersize',4,'linewidth',2)
legend('0 km', '9 km', '18 km', '30 km', '35 km', '62 km','location','northwest')
set(gca,'FontSize',16) %Set axis font size and limits
title ('YR150824 CDOM Absorption m^-1')
% figure(1)
% subplot(321)
% plot(YR150824_PAR(:,1),YR150824_PAR(:,2:5),'o-','Markersize',4,'linewidth',2)
% title('S5528-0 km')
% set(gca,'FontSize',16) %Set axis font size and limits
% 
% 
% subplot(322)
% plot(YR150824_PAR(:,1),YR150824_PAR(:,6:7),'o-','Markersize',4,'linewidth',2)
% title('S5529-9 km')
% set(gca,'FontSize',16) %Set axis font size and limits
% 
% 
% subplot(323)
% plot(YR150824_PAR(:,1),YR150824_PAR(:,8:11),'o-','Markersize',4,'linewidth',2)
% title('S5530-18 km')
% set(gca,'FontSize',16) %Set axis font size and limits
% 
% 
% subplot(324)
% plot(YR150824_PAR(:,1),YR150824_PAR(:,12:13),'o-','Markersize',4,'linewidth',2)
% title('S5531-30 km')
% set(gca,'FontSize',16) %Set axis font size and limits
% 
% 
% subplot(325)
% plot(YR150824_PAR(:,1),YR150824_PAR(:,14:15),'o-','Markersize',4,'linewidth',2)
% title('S5532-35 km')
% set(gca,'FontSize',16) %Set axis font size and limits
% 
% 
% subplot(326)
% plot(YR150824_PAR(:,1),YR150824_PAR(:,16:17),'o-','Markersize',4,'linewidth',2)
% title('S5533-62 km')
% set(gca,'FontSize',16) %Set axis font size and limits
