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get_data_plot_from_R_Circadian_Ultradian_v4_1.m
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get_data_plot_from_R_Circadian_Ultradian_v4_1.m
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%
% data_from_R = load('/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/UWS/result_mat_circ_5days.mat');
%
% [m,n] = size(data_from_R.data_circ_plot);
%
% dd_1 = data_from_R.data_circ_plot';
%
% t_plot = [1:1:m];
%
% figure
% y2_CC = mean(dd_1);
% z2_CC = std(dd_1)/sqrt (length(dd_1));
% errorbar(t_plot,y2_CC,z2_CC, 'b'); grid on;
% hold on
% y3_CC = mean (MCS_aux);
% z3_CC = std (MCS_aux)/sqrt (length(MCS_aux));
% errorbar (t_mcs, y3_CC,z3_CC, 'r'); grid on;
% title( 'Control (blue) vs MCS (red)')
% ylabel('Spectral Amplitude (SA)', 'FontSize',14,'FontWeight','bold','Color','k')
% xlabel('time (min)');
% MTN files
% MCS
clear all, close all, clc;
home = '/home/aldo/Documents/Projects/Avtivemeter/Data';
mcsp_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS+/'
mcsm_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS-/'
mcsast_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/MCS_ast/'
file_mat_LS_circ_4d = 'result_LombScarge_circ_4days.mat'
cd(mcsp_folder)
%MCS+
file_w = strcat(mcsp_folder,file_mat_LS_circ_4d);
data_LS_mcsp_awd = load(file_w)
dd_1 = data_LS_mcsp_awd.data_LS;
t_plot = dd_1(:,1);
figure, plot(t_plot/60, dd_1(:,2),'b'); grid on;
hold on;
% MCS-
file_w = strcat(mcsm_folder,file_mat_LS_circ_4d);
data_LS_mcsm_awd = load(file_w)
dd_1 = data_LS_mcsm_awd.data_LS;
t_plot = dd_1(:,1);
plot(t_plot/60, dd_1(:,2), 'r'); grid on;
hold on;
% MCS*
file_w = strcat(mcsast_folder,file_mat_LS_circ_4d);
data_LS_mcsast_awd = load(file_w)
dd_1 = data_LS_mcsast_awd.data_LS;
t_plot = dd_1(:,1);
plot(t_plot/60, dd_1(:,2), 'k'); grid on;
hold on;
title( 'Circadian - Lomb Scargle for MCS+, MCS- and MCS*', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (hours)','FontSize',14,'FontWeight','bold','Color','k')
legend({'MCS+', 'MCS-', 'MCS*'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
% UWS
UWS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_Files/UWS/'
file_mat_LS_circ_4d = 'result_LombScarge_circ_4days.mat'
cd(mcsp_folder)
%UWS
file_w = strcat(UWS_folder,file_mat_LS_circ_4d);
data_LS_UWS_mtn = load(file_w)
dd_1 = data_LS_UWS_mtn.data_LS;
t_plot = dd_1(:,1);
figure, plot(t_plot, dd_1(:,2));
hold on;
% AWD files
% MCS
clear all, close all, clc;
home = '/home/aldo/Documents/Projects/Avtivemeter/Data';
mcsp_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS+/'
mcsm_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS-/'
mcsast_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/MCS_ast/'
%file_mat_LS_circ_4d = 'result_LombScarge_circ_4days.mat' % for circadian
file_mat_LS_circ_4d = 'result_LombScarge_ultrad_4days.mat' % for ultradian
cd(home)
%MCS+
file_w = strcat(mcsp_folder,file_mat_LS_circ_4d);
data_LS_mcsp_awd = load(file_w)
dd_1 = data_LS_mcsp_awd.data_LS;
t_plot = dd_1(:,1);
figure, plot(t_plot, dd_1(:,2),'b'); grid on;
hold on;
% MCS-
file_w = strcat(mcsm_folder,file_mat_LS_circ_4d);
data_LS_mcsm_awd = load(file_w)
dd_1 = data_LS_mcsm_awd.data_LS;
t_plot = dd_1(:,1);
plot(t_plot, dd_1(:,2), 'r'); grid on;
hold on;
% MCS*
file_w = strcat(mcsast_folder,file_mat_LS_circ_4d);
data_LS_mcsast_awd = load(file_w)
dd_1 = data_LS_mcsast_awd.data_LS;
t_plot = dd_1(:,1);
plot(t_plot, dd_1(:,2), 'k'); grid on;
hold on;
title( 'Ultradian - Lomb Scargle for MCS+, MCS- and MCS*', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (minutes)','FontSize',14,'FontWeight','bold','Color','k')
legend({'MCS+', 'MCS-', 'MCS*'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
% UWS
UWS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/AWD_Files/Only_morning/UWS/'
file_mat_LS_circ_4d = 'result_LombScarge_circ_4days.mat'
cd(UWS_folder)
%UWS
file_w = strcat(UWS_folder,file_mat_LS_circ_4d);
data_LS_UWS_awd = load(file_w)
dd_1 = data_LS_UWS_awd.data_LS;
t_plot = dd_1(:,1);
figure, plot(t_plot, dd_1(:,2));
hold on;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% MCS and UWS of MTN and AWD together %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear all, close all, clc;
home = '/home/aldo/Documents/Projects/Avtivemeter/Data';
mcsp_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/acti_files_csv/4days/MCS_p/'
mcsm_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/acti_files_csv/4days/MCS_m/'
mcsast_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/acti_files_csv/4days/MCS_ast/'
%file_mat_LS_circ_4d = 'result_LombScarge_circ_4days.mat' % for circadian
file_mat_LS_circ_4d = 'result_LombScarge_ultrad_4days.mat' % for ultradian
cd(home)
%MCS+
file_w = strcat(mcsp_folder,file_mat_LS_circ_4d);
data_LS_mcsp_awd = load(file_w)
dd_1 = data_LS_mcsp_awd.data_LS;
t_plot = dd_1(:,1);
figure, plot(t_plot/60, dd_1(:,2),'b'); grid on;
hold on;
% MCS-
file_w = strcat(mcsm_folder,file_mat_LS_circ_4d);
data_LS_mcsm_awd = load(file_w)
dd_1 = data_LS_mcsm_awd.data_LS;
t_plot = dd_1(:,1);
plot(t_plot/60, dd_1(:,2), 'r'); grid on;
hold on;
% MCS*
file_w = strcat(mcsast_folder,file_mat_LS_circ_4d);
data_LS_mcsast_awd = load(file_w)
dd_1 = data_LS_mcsast_awd.data_LS;
t_plot = dd_1(:,1);
plot(t_plot/60, dd_1(:,2), 'k'); grid on;
hold on;
title( 'Ultradian - Lomb Scargle for MCS+, MCS- and MCS*', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (hours)','FontSize',14,'FontWeight','bold','Color','k')
legend({'MCS+', 'MCS-', 'MCS*'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Circadian for MCS, UWS%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
MCS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/'
UWS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/UWS/'
%file_mat_LS_circ_4d = 'result_LombScarge_circ_4days_2.mat'
% I did this to test the order of the file while is creating the mat file
file_mat_LS_circ_4d = 'result_LombScarge_circ_4days_5.mat' %
%MCS
% 95% CI ia 1.96 ; 90% CI 1.645
file_w = strcat(MCS_folder,file_mat_LS_circ_4d);
data_LS_MCS = load(file_w)
dd_1 = data_LS_MCS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
y_MCS = y_plot;
% YYY = [1:69];
% yyyy = repmat(YYY,163,1);
%
% surf(t_plot,yyyy,y_MCS);
figure
y2_CC = mean(y_plot,2);
z2_CC =1.96*(std(y_plot,1,2)/sqrt (length(y_plot)));
errorbar(t_plot(:,1)/60,y2_CC,z2_CC, 'b'); grid on;
hold on
AUC_mcs = [];
for i =1:n
AUC_mcs(i) = trapz(t_plot(:,i), y_plot(:,i));
end
%UWS
file_w = strcat(UWS_folder,file_mat_LS_circ_4d);
data_LS_UWS = load(file_w)
dd_1 = data_LS_UWS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
y_UWS = y_plot;
%surf(t_plot,yyyy,y_UWS);
y3_CC = mean(y_plot,2);
z3_CC = 1.96*(std (y_plot,1,2)/sqrt (length(y_plot)));
errorbar (t_plot(:,1)/60, y3_CC,z3_CC, 'r'); grid on;
title( 'Circadian - Lomb Scargle', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (hours)','FontSize',14,'FontWeight','bold','Color','k')
legend({'MCS', 'UWS'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
[m,n] = size(t_plot);
% AUC_uws = [];
% for i =1:n
% AUC_uws(i) = trapz(t_plot(:,i), y_plot(:,i));
%
% end
% p-value
% MCS vs UWS
[h_right,p_right]=ttest2(y2_CC,y3_CC, 0.05,'right') % p-value < 0.05
[h_left,p_left]=ttest2(y2_CC,y3_CC, 0.05,'left') %p-value = 1
% In this part of the code, I create a table and save it in a mat file,
% than then I will read it in Python to create nice plots :)
% The form of the table will be
% time MCS_power UWS_power
% table(:,1) = t_plot(:,1)/60;
% table(:,2) = y2_CC;
% table(:,3) = y3_CC;
%
% save('MCS_UWS_LombScargle.mat', 'table');
%
% load 'MCS_UWS_LombScargle.mat'
table_results.MCS(:,1) = t_plot(:,1)/60;
table_results.MCS(:,2) = y2_CC;
table_results.UWS(:,1) = t_plot(:,1)/60;
table_results.UWS(:,2) = y3_CC;
save('MCS_UWS_LombScargle.mat', 'table_results');
load 'MCS_UWS_LombScargle.mat'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Doing the statistics as Andrea's paper %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%periodicities to find
% period1 = 1440;
% period2 = 0.9*period1;
% period3 = 1.05*period1;
% period4 = 1.10*period1;
% period5 = 1.15*period1;
%
% index1 = find(t_plot == period1);
% index2 = find(t_plot == period2);
% index3 = find(t_plot == period3);
% index4 = find(t_plot == period4);
% index5 = find(t_plot == period5);
period1 = t_plot(106,1);
period2 = t_plot(109,1);
period3 = t_plot(112,1);
period4 = t_plot(115,1);
period5 = t_plot(120,1);
indx_T1 = 106;
indx_T2 = 109;
indx_T3 = 112;
indx_T4 = 115;
indx_T5 = 120;
power_at_period1_mcs = y_MCS(indx_T1,:);
power_at_period2_mcs = y_MCS(indx_T2,:);
power_at_period3_mcs = y_MCS(indx_T3,:);
power_at_period4_mcs = y_MCS(indx_T4,:);
power_at_period5_mcs = y_MCS(indx_T5,:);
power_at_period1_uws = y_UWS(indx_T1,:);
power_at_period2_uws = y_UWS(indx_T2,:);
power_at_period3_uws = y_UWS(indx_T3,:);
power_at_period4_uws = y_UWS(indx_T4,:);
power_at_period5_uws = y_UWS(indx_T5,:);
power_at_periods_mcs = [power_at_period1_mcs' power_at_period2_mcs' power_at_period3_mcs' power_at_period4_mcs' power_at_period5_mcs']
power_at_periods_uws = [power_at_period1_uws' power_at_period2_uws' power_at_period3_uws' power_at_period4_uws' power_at_period5_uws']
[h_right,p_right]=ttest2(power_at_periods_mcs,power_at_periods_uws, 0.05,'right') % p-value < 0.05
%[h_left,p_left]=ttest2(power_at_period1_mcs,power_at_period1_uws, 0.05,'left') %p-value = 1
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Ultradian for MCS, UWS%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clc, clear all, close all;
MCS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/'
UWS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/UWS/'
%file_mat_LS_circ_4d = 'result_LombScarge_ultra_4days_2.mat'
file_mat_LS_circ_4d = 'result_LombScarge_ultrd_4days_5.mat'
%cd(UWS_folder)
%MCS
file_w = strcat(MCS_folder,file_mat_LS_circ_4d);
data_LS_MCS = load(file_w);
dd_1 = data_LS_MCS.data_LS;
t_plot = dd_1(:,1:2:end);
% getting the data to plot between to and tf
% The following range was selected based on the previous report of
% rhythmicity
to = 120;
tf = 200;
index_t = find((t_plot(:,1) >to) & (t_plot(:,1) < tf));
y_plot = dd_1(:,2:2:end);
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
figure
y2_CC = mean(y_plot_idx,2);
z2_CC = 1.96*std(y_plot_idx,1,2)/sqrt(length(y_plot_idx));%1.96 for CI of 95%
errorbar(t_plot_idx,y2_CC,z2_CC, 'b'); grid on;
hold on
%UWS
file_w = strcat(UWS_folder,file_mat_LS_circ_4d);
data_LS_UWS = load(file_w);
dd_1 = data_LS_UWS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
% getting the data to plot between to and tf
index_t = find((t_plot(:,1) > to) & (t_plot(:,1) < tf));
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
y_plot_UWS = y_plot;
y3_CC = mean(y_plot_idx,2);
z3_CC = 1.96*std (y_plot_idx,1,2)/sqrt (length(y_plot_idx)); %1.96 for CI of 95%
errorbar (t_plot_idx, y3_CC,z3_CC, 'r'); grid on;
title( 'Ultradian - Lomb Scargle', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (min)','FontSize',14,'FontWeight','bold','Color','k')
legend({'MCS', 'UWS'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
% p-value
% MCS vs UWS
[h_right,p_right]=ttest2(y2_CC,y3_CC, 0.05,'right') % p-value < 0.05
[h_left,p_left]=ttest2(y2_CC,y3_CC, 0.05,'left') %p-value = 1
table_results.MCS(:,1) = t_plot(:,1);
table_results.MCS(:,2) = y2_CC;
table_results.UWS(:,1) = t_plot(:,1);
table_results.UWS(:,2) = y3_CC;
save('MCS_UWS_LombScargle_ultradian.mat', 'table_results');
load 'MCS_UWS_LombScargle_ultradian.mat'
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% MCS and UWS of MTN and AWD together %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Circadian for MCS, UWS, EMCS, LIS, Control%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clc, clear all, close all;
MCS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/'
UWS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/UWS/'
EMCS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/EMCS/'
LIS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/LIS/'
Control_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/Control/'
file_mat_LS_circ_4d = 'result_LombScarge_circ_4days_2.mat'
%MCS
file_w = strcat(MCS_folder,file_mat_LS_circ_4d);
data_LS_MCS = load(file_w)
dd_1 = data_LS_MCS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
[m,n] = size(t_plot);
y_MCS = y_plot;
%Compute the Area on the curve for every subject
AUC_mcs = [];
for i =1:n
AUC_mcs(i) = trapz(t_plot(:,i), y_plot(:,i));
end
%Compute the p-values for every periodicity
p_values_mcs = [];
for i =1:n
p_values_mcs(i) = trapz(t_plot(:,i), y_plot(:,i));
end
figure
y2_CC = mean(y_plot,2);
z2_CC = std(y_plot,1,2)/sqrt (length(y_plot));
errorbar(t_plot(:,1)/60,y2_CC,z2_CC, 'b'); grid on;
hold on
%UWS
file_w = strcat(UWS_folder,file_mat_LS_circ_4d);
data_LS_UWS = load(file_w)
dd_1 = data_LS_UWS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
y_UWS = y_plot;
[m,n] = size(t_plot);
%Compute the Area on the curve for every subject
AUC_uws = [];
for i =1:n
AUC_uws(i) = trapz(t_plot(:,i), y_plot(:,i));
end
y3_CC = mean(y_plot,2);
z3_CC = std (y_plot,1,2)/sqrt (length(y_plot));
errorbar (t_plot(:,1)/60, y3_CC,z3_CC, 'r'); grid on;
title( 'Circadian - Lomb Scargle', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (hours)','FontSize',14,'FontWeight','bold','Color','k')
hold on;
%EMCS
file_w = strcat(EMCS_folder,file_mat_LS_circ_4d);
data_LS_EMCS = load(file_w)
dd_1 = data_LS_EMCS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
y_MCS = y_plot;
y4_CC = mean(y_plot,2);
z4_CC = std(y_plot,1,2)/sqrt (length(y_plot));
errorbar(t_plot(:,1)/60,y4_CC,z4_CC, 'g'); grid on;
hold on
%LIS
file_w = strcat(LIS_folder,file_mat_LS_circ_4d);
data_LS_LIS = load(file_w)
dd_1 = data_LS_LIS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
y_MCS = y_plot;
y5_CC = mean(y_plot,2);
z5_CC = std(y_plot,1,2)/sqrt (length(y_plot));
errorbar(t_plot(:,1)/60,y5_CC,z5_CC, 'k'); grid on;
hold on
%Control
file_w = strcat(Control_folder,file_mat_LS_circ_4d);
data_LS_Control = load(file_w)
dd_1 = data_LS_Control.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
y_MCS = y_plot;
y6_CC = mean(y_plot,2);
z6_CC = std(y_plot,1,2)/sqrt (length(y_plot));
errorbar(t_plot(:,1)/60,y6_CC,z6_CC, 'm'); grid on;
legend({'MCS', 'UWS', 'EMCS', 'LIS', 'CONTROL'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
% p-value
% MCS vs UWS
[h_right,p_right]=ttest2(y2_CC,y3_CC, 0.05,'right') % p-value < 0.05
[h_left,p_left]=ttest2(y2_CC,y3_CC, 0.05,'left') %p-value = 1
[h_right,p_right,ci]=ttest2(y2_CC,y3_CC, [],[],'unequal') % p-value < 0.05
[h_left,p_left,ci]=ttest2(y2_CC,y3_CC, [],[],'unequal') %p-value = 1
% p-value of the AUC
[h_right,p_right]=ttest2(AUC_mcs,AUC_uws, 0.05,'right') % p-value < 0.05
[h_left,p_left]=ttest2(AUC_mcs,AUC_uws, 0.05,'left') %p-value = 1
% p-value for every time point
ri = []
for ii = 1: 100
ri(ii) = normrnd(0,1);
end
hist(ri)
[H,pVAlue, W] = swtest(ri)
[H,pVAlue, W] = swtest(y_MCS(2,:))
% This part checks if the data is normal or not normal using Shapiro test
H_vector = [];
for j=1:m
[H,pVAlue, W] = swtest(y_MCS(j,:));
H_vector(j) = H;
end
p_value_vector = [];
for j=1:m
[h_right,p_right]=wilcoxon(y_MCS(j,:),y_UWS(j,:));
p_value_vector(j) = p_right;
end
% Error bar plot
mean_values = [mean(y2_CC); % MCS
mean(y3_CC); % UWS
mean(y4_CC); % EMCS
mean(y5_CC); % LIS
mean(y6_CC)] ;% Control
stde_values = [std(y2_CC)/sqrt(length(y2_CC)); % MCS
std(y3_CC)/sqrt(length(y3_CC)); % UWS
std(y4_CC)/sqrt(length(y4_CC)); % EMCS
std(y5_CC)/sqrt(length(y5_CC)); % LIS
std(y6_CC)/sqrt(length(y6_CC))] ;% Control
% errorbar_groups(mean_values, stde_values, 'bar_names',{'MCS', 'UWS','EMCS', 'LIS', 'CONTROL'}, ...
% 'bar_width',0.75,'errorbar_width',0.5, ...
% 'optional_bar_arguments',{'LineWidth',1.5}, ...
% 'optional_errorbar_arguments',{'LineStyle','none','Marker','none','LineWidth',1.5});
%
% ylim([0 240])
%
% xlabel({'Circadian','(in minutes)'})
% legend('MCS', 'UWS');
%saving to a mat file
table_results.MCS(:,1) = t_plot(:,1);
table_results.MCS(:,2) = y2_CC;
table_results.UWS(:,1) = t_plot(:,1);
table_results.UWS(:,2) = y3_CC;
table_results.EMCS(:,1) = t_plot(:,1);
table_results.EMCS(:,2) = y4_CC;
table_results.LIS(:,1) = t_plot(:,1);
table_results.LIS(:,2) = y5_CC;
table_results.Control(:,1) = t_plot(:,1);
table_results.Control(:,2) = y6_CC;
save('MCS_UWS_all_LombScargle_circadian.mat', 'table_results');
%%%%%%%%%%%%%%
%% Ultradian %%
%%%%%%%%%%%%%%%
clc, clear all, close all;
MCS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/MCS/'
UWS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/UWS/'
EMCS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/EMCS/'
LIS_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/LIS/'
Control_folder = '/home/aldo/Documents/Projects/Avtivemeter/Files/MTN_AWD_Together/Control/'
file_mat_LS_circ_4d = 'result_LombScarge_ultra_4days_2.mat'
%cd(UWS_folder)
%MCS
file_w = strcat(MCS_folder,file_mat_LS_circ_4d);
data_LS_MCS = load(file_w);
dd_1 = data_LS_MCS.data_LS;
t_plot = dd_1(:,1:2:end);
% getting the data to plot between to and tf
% The following range was selected based on the previous report of
% rhythmicity
to = 120;
tf = 200;
index_t = find((t_plot(:,1) >to) & (t_plot(:,1) < tf));
y_plot = dd_1(:,2:2:end);
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
[m,n] = size(y_plot_idx);
%Compute the Area on the curve for every subject
AUC_mcs_ultr = [];
for i =1:n
AUC_mcs_ultr(i) = trapz(t_plot_idx, y_plot_idx(:,i));
end
figure
y2_CC = mean(y_plot_idx,2);
z2_CC = std(y_plot_idx,1,2)/sqrt(length(y_plot_idx));
errorbar(t_plot_idx,y2_CC,z2_CC, 'b'); grid on;
hold on
%UWS
file_w = strcat(UWS_folder,file_mat_LS_circ_4d);
data_LS_UWS = load(file_w);
dd_1 = data_LS_UWS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
% getting the data to plot between to and tf
index_t = find((t_plot(:,1) > to) & (t_plot(:,1) < tf));
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
[m,n] = size(y_plot_idx);
AUC_uws_ultr = [];
for i =1:n
AUC_uws_ultr(i) = trapz(t_plot_idx, y_plot_idx(:,i));
end
y_plot_UWS = y_plot;
y3_CC = mean(y_plot_idx,2);
z3_CC = std (y_plot_idx,1,2)/sqrt (length(y_plot_idx));
errorbar (t_plot_idx, y3_CC,z3_CC, 'r'); grid on;
title( 'Ultradian - Lomb Scargle', 'FontSize',14,'FontWeight','bold','Color','k')
ylabel('Power', 'FontSize',14,'FontWeight','bold','Color','k')
xlabel('time (min)','FontSize',14,'FontWeight','bold','Color','k')
hold on;
%EMCS
file_w = strcat(EMCS_folder,file_mat_LS_circ_4d);
data_LS_EMCS = load(file_w)
dd_1 = data_LS_EMCS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
% getting the data to plot between to and tf
index_t = find((t_plot(:,1) > to) & (t_plot(:,1) < tf));
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
%figure;
y4_CC = mean(y_plot_idx,2);
z4_CC = std (y_plot_idx,1,2)/sqrt (length(y_plot_idx));
errorbar (t_plot_idx, y4_CC,z4_CC, 'g'); grid on;
hold on;
%LIS
file_w = strcat(LIS_folder,file_mat_LS_circ_4d);
data_LS_LIS = load(file_w)
dd_1 = data_LS_LIS.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
% getting the data to plot between to and tf
index_t = find((t_plot(:,1) > to) & (t_plot(:,1) < tf));
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
y5_CC = mean(y_plot_idx,2);
z5_CC = std (y_plot_idx,1,2)/sqrt (length(y_plot_idx));
errorbar (t_plot_idx, y5_CC,z5_CC, 'k'); grid on;
hold on;
%Control
file_w = strcat(Control_folder,file_mat_LS_circ_4d);
data_LS_Control = load(file_w)
dd_1 = data_LS_Control.data_LS;
t_plot = dd_1(:,1:2:end);
y_plot = dd_1(:,2:2:end);
% getting the data to plot between to and tf
index_t = find((t_plot(:,1) > to) & (t_plot(:,1) < tf));
y_plot_idx = y_plot(index_t,:);
t_plot_idx = t_plot(index_t,1);
y6_CC = mean(y_plot_idx,2);
z6_CC = std (y_plot_idx,1,2)/sqrt (length(y_plot_idx));
errorbar (t_plot_idx, y6_CC,z6_CC, 'm'); grid on;
legend({'MCS', 'UWS', 'EMCS', 'LIS', 'CONTROL'},'FontWeight', 'bold', 'FontSize',12,'TextColor','black')
% p-value
% MCS vs UWS
[h_right,p_right]=ttest2(y2_CC,y3_CC, 0.05,'right') % p-value < 0.05
[h_left,p_left]=ttest2(y2_CC,y3_CC, 0.05,'left') %p-value = 1
% p-value of the AUC
[h_right,p_right]=ttest2(AUC_mcs_ultr,AUC_uws_ultr, 0.05,'right') % p-value < 0.05
[h_left,p_left]=ttest2(AUC_mcs_ultr,AUC_uws_ultr, 0.05,'left') %p-value = 1
%%%%
%saving to a mat file
table_results.MCS(:,1) = t_plot_idx;
table_results.MCS(:,2) = y2_CC;
table_results.UWS(:,1) = t_plot_idx;
table_results.UWS(:,2) = y3_CC;
table_results.EMCS(:,1) = t_plot_idx;
table_results.EMCS(:,2) = y4_CC;
table_results.LIS(:,1) = t_plot_idx;
table_results.LIS(:,2) = y5_CC;
table_results.Control(:,1) = t_plot_idx;
table_results.Control(:,2) = y6_CC;
save('MCS_UWS_all_LombScargle_ultradian.mat', 'table_results');
%% Computing the area under the curve and the statistics for it
%
%
% AUC: Area Under the Curve or tpz
%
%
%%%%%%%%%%%%
x = 0:0.1:4;
y = sqrt(4 - (x-2).^2);
figure, plot(x,y);
Area = trapz(x,y)
tpz_Control = trapz(Control_aux)/length(Control_aux);
tpz_EMCS = trapz(EMCS_aux)/length(EMCS_aux);
tpz_LIS = trapz(LIS_aux)/length(LIS_aux);
tpz_MCS = trapz(MCS_aux)/length(MCS_aux);
tpz_MCS_p = trapz(MCS_p_aux)/length(MCS_p_aux);
tpz_MCS_m = trapz(MCS_m_aux)/length(MCS_m_aux);
tpz_MCS_a = trapz(MCS_ast_aux)/length(MCS_ast_aux);
tpz_UWS = trapz(UWS_aux)/length(UWS_aux);