-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathFigure1_gams_no_uninfected.m
175 lines (157 loc) · 5.8 KB
/
Figure1_gams_no_uninfected.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
function [ttest_mat, plot_mat] = Figure1_gams_no_infected( early, late, g_names, species )
cd ..
cd results
mkdir ('gams_bar_charts')
cd gams_bar_charts
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,2)=mean(mol_early(k,d:d+8)); %*100;
std_dev=std(mol_early(k,d:d+8));
plot_std(k,2)=(std_dev/sqrt(9)); %*100;
plot_mat(k,5)=mean(mol_late(k,d:d+8)); %*100;
std_dev=std(mol_late(k,d:d+8));
plot_std(k,5)=(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=1:5;
for t=1:numel(y)
bar( y(t), plot_mat(k,t),1,'facecolor',colors(bar_color(t),:));
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', [1.5 4.5]); %iRBC gray, gametocyte black
set (gca, 'XTickLabel',x_label);
xlim([0 6]);
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