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Copy pathsat_length_gams_simplev2.m
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sat_length_gams_simplev2.m
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function [anova_sat, anova_chain, anova_combo, plot_combo, combo_text] = sat_length_gams_simplev2( mat, lipids, species, label, T, stat_yes )
%UNTITLED Summary of this function goes here
% % Detailed explanation goes here
% %
% mat=all;
% lipids=gam_text;
% label='gams';
% T=7;
% [r,c]=size(mat);
% stat_yes=0;
[r,c]=size(lipids);
group={'PL', 'SL', 'NL', 'DAG', 'APG'};
match_=cell2mat(species(:,3));
anova_sat=cell.empty;
anova_chain=cell.empty;
anova_combo=cell.empty;
a_count=1;
c_count=1;
co_count=1;
cd ..
cd results
mkdir saturation
cd saturation
for i=1:5
indx=find(match_==i);
L=species(indx,2);
saturation=double.empty;
chain_length=double.empty;
sum_=double.empty;
time_mat=double.empty;
col_label=double.empty;
levels=double.empty;
control_levels=double.empty;
n_=1;
NAME=group{i};
for k=1:length(L)
lipid=L{k}; %the name of the lipid we are including
[r,c]=size(lipids);
for j=1:r
text_=lipids{j,1};
text1=text_;
name='';
k_=strfind(text_,' ');
k1=(k_(1)-1);
for p_=1:k1
c_=text_(p_);
name=[name c_];
end
if strcmp (name, 'Acyl')==1 || strcmp(name, 'Lyso')==1
for m_=p_+1:p_+3
c_=text_(m_);
name=[name c_];
end
end
q=strfind(text_,':');
if numel(q)>0 && numel(q)<3
q1=q(1)-1;
else
q1=0;
end
if strcmp(name,lipid)==1 %same family
%look at the chain length
if q1>0
chain='';
sat_='';
Q=strfind(text_, '/');
P=strfind(text_,'-');
if numel(Q)>0
%q1=q(2)-1;
rL=Q-1;
elseif numel(P)>0
%q1=q(2)-1;
rL=P(1)-1;
else
rL=length(text_);
end
for p_=q1-1:q1
c_=text_(p_);
chain=[chain c_] ;
end
chain = str2num(chain);
%chain_length(n_,1)=chain;
for p_=q1+2:rL
c_=text_(p_) ;
sat_=[sat_ c_];
end
sat_=str2num(sat_);
% saturation(n_,1)=sat_;
%FOR ADDING SECOND NUMBER -----------------
rL=length(text_);
if numel(Q)>0
q2=q(2)-1;
%rL=Q-1;
elseif numel(P)>0
q2=q(2)-1;
%rL=P-1;
else
q2=0;
end
if i==2 %PL
chain2='';
sat2='';
for p_=q2-1:q2
c_=text_(p_);
chain2=[chain2 c_] ;
end
chain2 = str2num(chain2);
chain_length(n_,1)=chain + chain2;
for p_=q2+2:rL
c_=text_(p_) ;
sat2=[sat2 c_];
end
sat2=str2num(sat2);
saturation(n_,1)=sat_+sat2;
elseif numel(P)>0
chain2='';
sat2='';
for p_=q2-1:q2
c_=text_(p_);
chain2=[chain2 c_] ;
end
chain2 = str2num(chain2);
chain_length(n_,1)=chain2;
for p_=q2+2:rL
c_=text_(p_) ;
sat2=[sat2 c_];
end
sat2=str2num(sat2);
saturation(n_,1)=sat2;
else
chain_length(n_,1)=chain;
saturation(n_,1)=sat_;
end
levels(n_,:)=mat(j,:);
col_label{n_,1}=text1;
n_=n_+1;
end
end
end
end
%make an average with time for each member of the group
[r1,c1]=size(levels);
levels_sum=nansum(levels);
levels_percent=zeros(r1,c1);
for k2=1:r1
for j2=1:c1
levels_percent(k2,j2)=(levels(k2,j2)/levels_sum(j2))*100;
end
end
if T>1 %% ALL EXCEPT FOR CONTROL
for k2=1:r1
d=1;
for j=1:T
time_mat(k2,j)=nanmean(levels(k2,d:d+8));
d=d+9;
end
end
sum_=nansum(time_mat);
unique_sat=unique(saturation);
plot_sat=zeros(length(unique_sat),T);
text_sat=double.empty;
text_length=double.empty;
stat_mat=double.empty;
for j=1:length(unique_sat)
u=unique_sat(j);
anova_sat{a_count,1}=group{i};
anova_sat{a_count,2}=u;
indx=find(saturation==u); %find the same saturation level
lipid_new=time_mat(indx,:);
[rl,cl]=size(lipid_new);
if rl>1
lipid_sum=nansum(lipid_new);
else
lipid_sum=lipid_new;
end
for j2=1:T
plot_sat(j,j2)=(lipid_sum(j2)/sum_(j2))*100;
end
text_sat(j)=u;
stat_sat=levels_percent(indx,:);
stat_mat=double.empty;
[r3,c3]=size(stat_sat);
if r3>1
stat_sat=nansum(stat_sat);
end
d=1;
for j2=1:T
temp=stat_sat(d:d+8);
stat_mat(:,j2)=temp;
d=d+9;
end
if stat_yes==1
p_sat=anova1(stat_mat);
close all
else
p_stat='NA';
end
anova_sat{a_count,3}=p_stat;
temp_ttest=[];
for n=1:T
group1=stat_mat(:,n);
for m=(n+1):T
group2=stat_mat(:,m);
[hval,pval]=ttest2(group1,group2);
if pval<0.01
temp_ttest=[temp_ttest n m];
end
end
end
L_t=length(temp_ttest);
temp3='';
for J=1:2:L_t
temp1=num2str(temp_ttest(J));
temp2=num2str(temp_ttest(J+1));
temp3=[temp3 temp1 '/' temp2 ','];
end
anova_sat{a_count,4}=temp3;
if isempty(temp3)==1
anova_sat{a_count,4}='NA';
end
a_count=a_count+1;
end
unique_length=unique(chain_length);
plot_length=zeros(length(unique_length),T);
for j=1:length(unique_length)
u=unique_length(j);
anova_chain{c_count,1}=group{i};
anova_chain{c_count,2}=u;
indx=find(chain_length==u); %find the same saturation level
lipid_new=time_mat(indx,:);
[rl,c1]=size(lipid_new);
if rl>1
lipid_sum=nansum(lipid_new);
else
lipid_sum=lipid_new;
end
for j2=1:T
plot_length(j,j2)=(lipid_sum(j2)/sum_(j2))*100;
end
text_length(j)=u;
stat_chain=levels_percent(indx,:);
stat_mat=double.empty;
[r3,c3]=size(stat_chain);
if r3>1
stat_chain=nansum(stat_chain);
end
d=1;
for j2=1:T
temp=stat_chain(d:d+8);
stat_mat(:,j2)=temp;
d=d+9;
end
if stat_yes==1
p_chain=anova1(stat_mat);
close all
else
p_chain='NA';
end
anova_chain{c_count,3}=p_chain;
temp_ttest=[];
for n=1:T
group1=stat_mat(:,n);
for m=(n+1):T
group2=stat_mat(:,m);
[hval,pval]=ttest2(group1,group2);
if pval<0.01
temp_ttest=[temp_ttest n m];
end
end
end
L_t=length(temp_ttest);
temp3='';
for J=1:2:L_t
temp1=num2str(temp_ttest(J));
temp2=num2str(temp_ttest(J+1));
temp3=[temp3 temp1 '/' temp2 ','];
end
anova_chain{c_count,4}=temp3;
if isempty(temp3)==1
anova_chain{c_count,4}='NA';
end
c_count=c_count+1;
end
plot_combo=double.empty;
count=1;
for j=1:length(unique_sat)
us=unique_sat(j);
indxs=find(saturation==us);
for j2=1:length(unique_length)
error=0;
ul=unique_length(j2);
indxl=find(chain_length==ul);
indx=intersect(indxl,indxs);
if numel(indx)==0
error=1;
elseif numel(indx)>1
lipid_new=nansum(time_mat(indx,:));
else
lipid_new=time_mat(indx,:);
end
if error==0
[rl,c1]=size(lipid_new);
if rl>1
lipid_sum=nansum(lipid_new);
else
lipid_sum=lipid_new;
end
for j3=1:T
plot_combo(count,j3)=(lipid_sum(j3)/sum_(j3))*100;
end
text_combo(count,1)=us;
text_combo(count,2)=ul;
count=count+1;
%STATS COMBO------------------------
anova_combo{co_count,1}=group{i};
anova_combo{co_count,2}=ul;
anova_combo{co_count,3}=us;
stat_combo=levels_percent(indx,:);
stat_mat=double.empty;
[r3,c3]=size(stat_combo);
if r3>1
stat_combo=nansum(stat_combo);
end
d=1;
for j3=1:T
temp=stat_combo(d:d+8);
stat_mat(:,j3)=temp;
d=d+9;
end
if stat_yes==1
p_chain=anova1(stat_mat);
close all
else
p_chain='NA';
end
anova_combo{co_count,4}=p_chain;
temp_ttest=[];
for n=1:T
group1=stat_mat(:,n);
for m=(n+1):T
group2=stat_mat(:,m);
[hval,pval]=ttest2(group1,group2);
if pval<0.01
temp_ttest=[temp_ttest n m];
end
end
end
L_t=length(temp_ttest);
temp3='';
for J=1:2:L_t
temp1=num2str(temp_ttest(J));
temp2=num2str(temp_ttest(J+1));
temp3=[temp3 temp1 '/' temp2 ','];
end
anova_combo{co_count,5}=temp3;
if isempty(temp3)==1
anova_combo{co_count,5}='NA';
end
co_count=co_count+1;
end
end
end
%plot the length levels
[r3,c3]=size(plot_length);
plot_length_=zeros(7,4);
for S=1:r3
if text_length(S)<=12
plot_length_(:,1)=plot_length_(:,1)+ plot_length(S,:)';
elseif text_length(S)>12 && text_length(S)<=24
plot_length_(:,2)=plot_length_(:,2)+ plot_length(S,:)';
elseif text_length(S)<42
plot_length_(:,3)=plot_length_(:,3)+ plot_length(S,:)';
else
plot_length_(:,4)=plot_length_(:,4)+plot_length(S,:)';
end
end
f1=subplot(7,1,1);
bar(1:4, plot_length_(1,:));
set(gca, 'XTickLabel', '');
ylim([0 100]);
ylabel('Control');
title(['% of ' NAME ' with chain length']);
f2=subplot(7,1,2);
bar(1:4,plot_length_(2,:));
set(gca, 'XTickLabel', '');
ylim([0 100]);
ylabel('Early-Parasite');
linkaxes([f1 f2],'x'); %make y axis the same
pos1=get(f1,'Position'); %find the current position [x,y,width,height]
pos2=get(f2,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f2,'Position',pos2);
f3=subplot(7,1,3);
bar(1:4,plot_length_(3,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Early-Infected');
linkaxes([f2 f3],'x'); %make y axis the same
pos1=get(f2,'Position'); %find the current position [x,y,width,height]
pos2=get(f3,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f3,'Position',pos2);
f4=subplot(7,1,4);
bar(1:4,plot_length_(4,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Early-Uninfected');
linkaxes([f3 f4],'x'); %make y axis the same
pos1=get(f3,'Position'); %find the current position [x,y,width,height]
pos2=get(f4,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f4,'Position',pos2);
f5=subplot(7,1,5);
bar(1:4,plot_length_(5,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Late-Parasite');
linkaxes([f4 f5],'x'); %make y axis the same
pos1=get(f4,'Position'); %find the current position [x,y,width,height]
pos2=get(f5,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f5,'Position',pos2);
f6=subplot(7,1,6);
bar(1:4,plot_length_(6,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Late-Infected');
linkaxes([f5 f6],'x'); %make y axis the same
pos1=get(f5,'Position'); %find the current position [x,y,width,height]
pos2=get(f6,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f6,'Position',pos2);
f7=subplot(7,1,7);
bar(1:4,plot_length_(7,:));
ylim([0 100]);
set(gca, 'XTickLabel', {'Short', 'Medium', 'Long', 'Very Long'});
ylabel('Late-UnInfected');
linkaxes([f6 f7],'x'); %make y axis the same
pos1=get(f6,'Position'); %find the current position [x,y,width,height]
pos2=get(f7,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f7,'Position',pos2);
print (gcf, '-dpng', [label '_' NAME '_length_simple.png']);
print (gcf, '-depsc2', [label '_' NAME '_length_simple.eps']);
close
%plot the saturation levels
[r3,c3]=size(plot_sat);
plot_sat_=zeros(7,3);
for S=1:r3
if text_sat(S)==0
plot_sat_(:,1)=plot_sat_(:,1)+ plot_sat(S,:)';
elseif text_sat(S)==1
plot_sat_(:,2)=plot_sat_(:,2)+ plot_sat(S,:)';
elseif text_sat(S)>1
plot_sat_(:,3)=plot_sat_(:,3)+ plot_sat(S,:)';
else
text_sat(S)
end
end
f1=subplot(7,1,1);
bar(1:3, plot_sat_(1,:));
set(gca, 'XTickLabel', '');
ylim([0 100]);
ylabel('Control');
title(['% of ' NAME ' with saturation level']);
f2=subplot(7,1,2);
bar(1:3, plot_sat_(2,:));
set(gca, 'XTickLabel', '');
ylim([0 100]);
ylabel('Early-Parasite');
linkaxes([f1 f2],'x'); %make y axis the same
pos1=get(f1,'Position'); %find the current position [x,y,width,height]
pos2=get(f2,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f2,'Position',pos2);
f3=subplot(7,1,3);
bar(1:3, plot_sat_(3,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Early-Infected');
linkaxes([f2 f3],'x'); %make y axis the same
pos1=get(f2,'Position'); %find the current position [x,y,width,height]
pos2=get(f3,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f3,'Position',pos2);
f4=subplot(7,1,4);
bar(1:3, plot_sat_(4,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Early-Uninfected');
linkaxes([f3 f4],'x'); %make y axis the same
pos1=get(f3,'Position'); %find the current position [x,y,width,height]
pos2=get(f4,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f4,'Position',pos2);
f5=subplot(7,1,5);
bar(1:3, plot_sat_(5,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Late-Parasite');
linkaxes([f4 f5],'x'); %make y axis the same
pos1=get(f4,'Position'); %find the current position [x,y,width,height]
pos2=get(f5,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f5,'Position',pos2);
f6=subplot(7,1,6);
bar(1:3, plot_sat_(6,:));
ylim([0 100]);
set(gca, 'XTickLabel', '');
ylabel('Late-Infected');
linkaxes([f5 f6],'x'); %make y axis the same
pos1=get(f5,'Position'); %find the current position [x,y,width,height]
pos2=get(f6,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f6,'Position',pos2);
f7=subplot(7,1,7);
bar(1:3, plot_sat_(7,:));
ylim([0 100]);
ylabel('Late-UnInfected');
linkaxes([f6 f7],'x'); %make y axis the same
pos1=get(f6,'Position'); %find the current position [x,y,width,height]
pos2=get(f7,'Position'); %find the current position [x,y,width,height]
pos2(2)=pos1(2) - pos2(4); %move the second so it touches the first
set (f7,'Position',pos2);
set(gca, 'XTickLabel', {'SAT', 'MUFA', 'PUFA'});
print (gcf, '-dpng', [label '_' NAME '_saturation_simple.png']);
print (gcf, '-depsc2', [label '_' NAME '_saturation_simple.eps']);
close
end
end
end