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function_run_model.m
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function_run_model.m
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% Drive file
% hr time units
% define simulation times
function function_run_model(data_dictionary,virus_inoculation,IC_dAT,line_index)
TSTART = 0;
TSTOP = 1200*24; % n days to hours
Ts = 0.1;
TSIM = (TSTART:Ts:TSTOP);
mw = data_dictionary.mw;
[T,X] = SolveBalances(TSTART,TSTOP,Ts,data_dictionary);
data_dictionary.initial_condition = X(end,:);
data_dictionary.initial_condition(1) = virus_inoculation; % load virus
if IC_dAT ~= 0
data_dictionary.initial_condition(5) = IC_dAT; % load virus
data_dictionary.initial_condition(6) = IC_dAT; % load virus
end
% %
% % call solver
TSTART = TSTOP;
TSTOP2 = TSTOP+75*24+75*24;
T2=0;
[T2,X2] = SolveBalances(TSTART,TSTOP2,Ts,data_dictionary);
% %
T_basal = T;
X_basal = X;
T_virus = [T_basal;T2];
X_virus = [X_basal;X2];
T = [T_virus-TSTOP];
X = [X_virus];
for species_index = 1:length(data_dictionary.initial_condition)
s.(data_dictionary.species_names(species_index,2)) = X(:,species_index);
end
% Set colormap
cmap = [202 0 32
0.2422*255 0.1504*255 0.6603*255
217 95 2
0 0 0]/255;
% Normalization variables
dAT2maxn = 3.0177e+06;
dAT1maxn = 2.2133e+06;
Imaxn = 1.9772e+09;
figure(1)
subplot(3,2,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.V,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel({'Viral Load'; '(RNA molecules/mL)'})
xlabel('Days')
hold on
xlim([-25 75])
set(gca, 'YScale', 'log')
ylim([1e4 1e12])
yticks([1e4 1e6 1e8 1e10 1e12])
subplot(3,2,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.AT2/s.AT2(1),'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('AT2 (#)')
xlabel('Days')
hold on
xlim([-25 75])
set(gca, 'YScale', 'linear')
subplot(3,2,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.I/Imaxn,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Infected (#)')
xlabel('Days')
hold on
xlim([-25 75])
set(gca, 'YScale', 'linear')
subplot(3,2,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.AT1/s.AT1(1),'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('AT1 (#)')
xlabel('Days')
hold on
xlim([-25 75])
set(gca, 'YScale', 'linear')
subplot(3,2,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.dAT1/dAT1maxn,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Damaged AT1 (#)')
xlabel('Days')
hold on
xlim([-25 75])
set(gca, 'YScale', 'log')
ylim([1e2 1e11])
yticks([1e2 1e4 1e6 1e8 1e10])
subplot(3,2,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.dAT2/dAT2maxn,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Damaged AT2 (#)')
xlabel('Days')
hold on
xlim([-25 75])
set(gca, 'YScale', 'log')
ylim([1e2 1e11])
yticks([1e2 1e4 1e6 1e8 1e10])
figure(4)
subplot(3,4,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL6_c*mw.il6,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IL6 plasma (pg/mL) ')
xlabel('Days')
subplot(3,4,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.TNFa_c*mw.tnfa,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('TNFa plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL12_c*mw.il2,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IL12 plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNb_c*mw.ifnb,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IFNb plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNg_c*mw.ifng,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IFNg plasma (pg/ml)')
xlabel('Days')
hold on
subplot(3,4,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL10_c*mw.il10,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('IL10 plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,7)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL17_c*mw.il17,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IL17 plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,8)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL2_c*mw.il2,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('IL2 plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,9)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL1b_c*mw.il1b,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IL1b plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,10)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.TGFb_c*mw.tgfb,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('TGFb plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,11)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.GMCSF_c*mw.gmcsf,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('GMCSF plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
vol_alv_ml = data_dictionary.vol_alv_ml;
vol_plasma = data_dictionary.vol_plasma;
% convert total cell count to #/uL
%% data is in billion cells / L
cell2conclung = 1/vol_alv_ml/1000; % cells --> cells/uL
cell2concplasma = 1/1000; % cells/mL --> cells/uL
billioncellsperL2cellsperuL = 1e9/1e6;
figure(6)
subplot(3,3,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.pDC_c/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('pDC plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.M1_c/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('M1 plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.N_c/1000+data_dictionary.iN,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('N plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1_c/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Th1 plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th17_c/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Th17 plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.CTL_c/1000+data_dictionary.iCD8,'LineWidth',2.5,'Color',ax.ColorOrder (line_index,:))
hold on
ylabel('CTL plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,7)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Treg_c/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Treg plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,8)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1_c/1000+s.Th17_c/1000+s.Treg_c/1000 + data_dictionary.iCD4,'LineWidth',2.5, 'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('CD4 plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,9)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1_c/1000+s.Th17_c/1000+s.Treg_c/1000+s.CTL_c/1000+data_dictionary.iCD4 +data_dictionary.iCD4,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('CD3 plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
figure(3)
subplot(2,4,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL6_c*mw.il6,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IL6 plasma (pg/mL) ')
xlabel('Days')
hold on
subplot(2,4,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNb_c*mw.ifnb,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Type I IFN plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(2,4,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNg_c*mw.ifng,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IFN\gamma plasma (pg/ml)')
xlabel('Days')
hold on
subplot(2,4,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL10_c*mw.il10,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('IL10 plasma (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(2,4,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL6/vol_alv_ml*mw.il6,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IL6 lung (pg/mL) ')
xlabel('Days')
hold on
subplot(2,4,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNb/vol_alv_ml*mw.ifnb,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Type I IFN lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(2,4,7)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNg/vol_alv_ml*mw.ifng,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IFN\gamma lung (pg/ml)')
xlabel('Days')
hold on
subplot(2,4,8)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL10/vol_alv_ml*mw.il10,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('IL10 lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
figure(5)
subplot(2,4,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.pDC_c/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Total DC plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 180])
subplot(2,4,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.N_c/1000+data_dictionary.iN,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Total N plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 3200])
subplot(2,4,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1_c/1000+s.Th17_c/1000+s.Treg_c/1000 + data_dictionary.iCD4,'LineWidth',2.5, 'Color',ax.ColorOrder(line_index,:))
hold on
ylabel({'Total CD4+';'T cells plasma (#/\muL)'})
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 1000])
subplot(2,4,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.CTL_c/1000+data_dictionary.iCD8,'LineWidth',2.5,'Color',ax.ColorOrder (line_index,:))
hold on
ylabel('Total CTL plasma (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 1000])
subplot(2,4,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.pDC/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Activated DC lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 180])
subplot(2,4,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.N/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Activated N lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 3200])
subplot(2,4,7)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1/vol_alv_ml/1000+s.Th17/vol_alv_ml/1000+s.Treg/vol_alv_ml/1000 ,'LineWidth', 2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel({'Activated CD4+';' T cells lung (#/\muL)'})
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 1000])
subplot(2,4,8)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.CTL/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Activated CTL lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
ylim([0 1000])
figure(7)
subplot(3,3,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.pDC/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('pDC lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.M1/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('M1 lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.N/vol_alv_ml/1000+data_dictionary.iN,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('N lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Th1 lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th17/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Th17 lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.CTL/vol_alv_ml/1000+data_dictionary.iCD8,'LineWidth',2.5,'Color',ax.ColorOrder (line_index,:))
hold on
ylabel('CTL lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,7)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Treg/vol_alv_ml/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('Treg lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,8)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1/vol_alv_ml/1000+s.Th17/vol_alv_ml/1000+s.Treg/vol_alv_ml/1000 + data_dictionary.iCD4,'LineWidth',2.5, 'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('CD4 lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,3,9)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.Th1/vol_alv_ml/1000+s.Th17/vol_alv_ml/1000+s.Treg/vol_alv_ml/1000+s.CTL/vol_alv_ml/1000+data_dictionary.iCD4 +data_dictionary.iCD4,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('CD3 lung (#/\muL)')
xlabel('Days')
hold on
xlim([-25 75])
figure(8)
subplot(3,4,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL6/vol_alv_ml*mw.il6,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IL6 lung (pg/mL) ')
xlabel('Days')
subplot(3,4,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.TNFa/vol_alv_ml*mw.tnfa,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('TNFa lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL12/vol_alv_ml*mw.il2,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IL12 lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNb/vol_alv_ml*mw.ifnb,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IFNb lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,5)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IFNg/vol_alv_ml*mw.ifng,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
xlim([-25 75])
ylabel('IFNg lung (pg/ml)')
xlabel('Days')
hold on
subplot(3,4,6)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL10/vol_alv_ml*mw.il10,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('IL10 lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,7)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL17/vol_alv_ml*mw.il17,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IL17 lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,8)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL2/vol_alv_ml*mw.il2,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('IL2 lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,9)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.IL1b/vol_alv_ml*mw.il1b,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('IL1b lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,10)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.TGFb/vol_alv_ml*mw.tgfb,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('TGFb lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
subplot(3,4,11)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.GMCSF/vol_alv_ml*mw.gmcsf,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
ylabel('GMCSF lung (pg/ml)')
xlabel('Days')
hold on
xlim([-25 75])
figure(11)
subplot(2,2,1)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24, s.Blood_CRP*mw.crp/1000,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:)) % s.Blood_CRP*mw.crp/1000 to convert to mg/L units
hold on
ylabel('Blood CRP mg/L')
xlabel('Days')
xlim([-25 75])
subplot(2,2,2)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.FER_c*mw.fer,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Ferritin plasma ug/L')
xlabel('Days')
xlim([-25 75])
subplot(2,2,3)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.SPD*mw.spd/vol_alv_ml,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Surfactant Protein D lung ng/mL ')
xlabel('Days')
xlim([-25 75])
subplot(2,2,4)
ax = gca;
ax.LineStyleOrder = {'-','-','-.','-.'};
ax.LineStyleOrderIndex = line_index;
ax.ColorOrder = [cmap(2,:);cmap(3,:);cmap(4,:);cmap(1,:)];
plot(T/24,s.SPD_c*mw.spd,'LineWidth',2.5,'Color',ax.ColorOrder(line_index,:))
hold on
ylabel('Surfactant Protein D plasma ng/mL')
xlabel('Days')
xlim([-25 75])
end