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Copy pathFigure1_gams_no_infected.m
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Figure1_gams_no_infected.m
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function [ttest_mat, plot_mat] = Figure1_gams_no_infected( early, late, g_names, species )
cd ..
cd results
mkdir ('gams_bar_charts_noinf')
cd gams_bar_charts_noinf
g_groups=cell2mat(g_names(:,2));
unique_=unique(g_groups);
indx=find(unique_~=0);
unique_=unique_(indx);
cmap=[255/255 51/255 51/255; 0/255 204/255 102/255; 204/255 0/255 204/255];
L_=length(unique_);
[r,c]=size(early);
mol_early=zeros(L_,c);
sum_early=sum(early);
mol_late=zeros(L_,c);
sum_late=sum(late);
%find the mol%time for each lipid group
for k=1:length(unique_);
indx=find(g_groups==unique_(k));
mat_e=early(indx,:);
mat_species_e=sum(mat_e);
mat_l=late(indx,:);
mat_species_l=sum(mat_l);
% for j=1:c
mol_early(k,:)=mat_species_e; %/sum_early(1,j);
mol_late(k,:)=mat_species_l;%/sum_late(1,j);
%end
% indx=find(c1_groups==unique_(k));
% mat_c1=control1(indx,:);
% mat_species_c1=sum(mat_c1);
% indx=find(c2_groups==unique_(k));
% mat_c2=control2(indx,:);
% mat_species_c2=sum(mat_c2);
% for j=1:3
% mol_t4(k,j)=mat_species_c1(1,j)/sum_c1(1,j);
% mol_t4(k,j+3)=mat_species_c2(1,j)/sum_c2(1,j);
% end
end
ttest_mat=cell(length(unique_)+1,8);
ttest_mat{1,2}='E vs. L parasite';
ttest_mat{1,3}='E vs. L iRBC';
ttest_mat{1,4}='E vs. L uiRBC';
ttest_mat{1,5}='E-gam vs. E-iRBC';
ttest_mat{1,6}='E-gam vs. E-uiRBC';
ttest_mat{1,7}='L-gam vs. L-iRBC';
ttest_mat{1,8}='L-gam vs. L-uiRNC';
ttest_mat{1,9}='E-iRBC vs. E-uiRBC';
ttest_mat{1,10}='L-iRBC vs. L-uiRBC';
plot_mat=zeros(L_,7);
plot_std=NaN(L_,7);
mol_names=cell(length(unique_),1);
l_malaria=mol_late(:,1:9);
l_infected=mol_late(:,10:18);
l_uninf=mol_late(:,19:27);
e_malaria=mol_early(:,1:9);
e_infected=mol_early(:,10:18);
e_uninf=mol_early(:,19:27);
for k=1:length(unique_);
label=species{unique_(k),2};
mol_names{k,1}=label;
ttest_mat{k+1,1}=label;
c=1;
d=1;
for j=1:3
if j==1 %gametocytes
plot_mat(k,1)=mean(mol_early(k,d:d+8)); %*100;
std_dev=std(mol_early(k,d:d+8));
plot_std(k,1)=(std_dev/sqrt(9)); %*100;
plot_mat(k,3)=mean(mol_late(k,d:d+8)); %*100;
std_dev=std(mol_late(k,d:d+8));
plot_std(k,3)=(std_dev/sqrt(9)); %*100;
elseif j==2 %iRBC
% plot_mat(k,1)=mean(mol_early(k,d:d+8)); %*100;
% std_dev=std(mol_early(k,d:d+8));
% plot_std(k,1)=(std_dev/sqrt(9)); %*100;
% plot_mat(k,4)=mean(mol_late(k,d:d+8)); %*100;
% std_dev=std(mol_late(k,d:d+8));
% plot_std(k,4)=(std_dev/sqrt(9)); %*100;
else
u=cat(2, mol_early(k,d:d+8), mol_late(k,d:d+8)) ;
uiRBC(k,1)=mean(u) ;
std_uiRBC=std(u);
uiRBC(k,2)=std_uiRBC/sqrt(18);
end
[h,p]=ttest(mol_early(k,d:d+8),mol_late(k,d:d+8));
ttest_mat{k+1,j+1}=p;
d=d+9;
end
[h,p]=ttest(e_malaria(k,:), e_infected(k,:));
ttest_mat{k+1,5}=p;
[h,p]=ttest(e_malaria(k,:), e_uninf(k,:));
ttest_mat{k+1,6}=p;
[h,p]=ttest(l_malaria(k,:), l_infected(k,:));
ttest_mat{k+1,7}=p;
[h,p]=ttest(l_malaria(k,:), l_uninf(k,:));
ttest_mat{k+1,8}=p;
[h,p]=ttest(e_infected(k,:), e_uninf(k,:));
ttest_mat{k+1,9}=p;
[h,p]=ttest(l_infected(k,:), l_uninf(k,:));
ttest_mat{k+1,10}=p;
colors=[0 0 0; 0.5 0.5 0.5; 1 1 1];
%bar_color=[2 1 1 2 1];
y=1:3;
for t=1:numel(y)
bar( y(t), plot_mat(k,t),1,'facecolor','k');
hold on
h(t)=errorbar (y(t),plot_mat(k,t),plot_std(k,t)); %,'.k', 'MarkerSize',2, 'linewidth',2 );
end
% Perform the correction
for ii=1:length(h)
hc = (get(h(ii),'Children'))';
% Get the x-coordinates for all children
xdata = get(hc(2),'XData');
% Build arrays to select the proper x-coord. for all whiskers
% temp contains all indeces for the left x-coord of the whiskers
temp = 4:3:length(xdata);
temp(3:3:end) = [];
% temp2 contains the indeces for the original data point (where the whiskers are drawn around)
temp2=sort([1:9:length(xdata), 2:9:length(xdata)]);
% Build vectors containing indeces for the left and right x- coordinates of the whiskers
xleft = temp; xright = temp+1;
% Write the new data for the x-coordinates of the whiskers (original data point +- 0.01)
xdata(xleft) = xdata(temp2) - 0.01;
xdata(xright) = xdata(temp2) + 0.01;
% Set the new coordinates in the graph
set(hc(2),'Xdata',xdata, 'Color', 'k', 'LineWidth', 2)
end
title(label, 'fontsize', 18);
x_control=0:10:30;
control=uiRBC(k,1);
control_up=uiRBC(k,1)+uiRBC(k,2);
control_down=uiRBC(k,1)-uiRBC(k,2);
y_control=[control control control control];
y_control_up=[control_up control_up control_up control_up];
y_control_down=[control_down control_down control_down control_down];
plot(x_control, y_control, 'r-', 'linewidth', 2);
plot(x_control, y_control_up, 'r--', 'linewidth',2);
plot(x_control, y_control_down, 'r--', 'linewidth', 2);
hold off
%x_label= {'Gametocyte','iRBC', [],'Gametocyte','iRBC'};
x_label={'Early', 'Late'};
set(gca, 'XTick', [1 3]); %iRBC gray, gametocyte black
set (gca, 'XTickLabel',x_label);
xlim([0 4]);
set(gca,'FontSize',18, 'linewidth',2);
%NumTicks = 4;
%L = get(gca,'YLim');
%set(gca,'YTick',linspace(L(1),L(2),NumTicks))
%ylabel('Mol % of Total Lipids Measured');
print (gcf, '-depsc2', [label '_gametocyte_bar.eps']);
print (gcf, '-dpng', [label '_gametocyte_bar.png']);
close all
end
cd ..
cd ..
cd programs
end