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sat_length_gamsv2.m
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function [anova_sat, anova_chain, anova_combo, plot_combo, combo_text] = sat_length_gamsv2( mat, lipids, species, label, T )
%UNTITLED Summary of this function goes here
% % Detailed explanation goes here
%
% mat=all;
% lipids=gam_text;
% label='gams';
% T=3;
[r,c]=size(mat);
[r,c]=size(lipids);
group={'PL', 'SL', 'NL', 'DAG'};
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=1:4
indx=find(match_==i);
L=species(indx,2);
saturation=double.empty;
chain_length=double.empty;
time_mat=double.empty;
col_label=double.empty;
levels=double.empty;
n_=1;
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);
for p_=q1+2:rL
c_=text_(p_) ;
sat_=[sat_ c_];
end
sat_=str2num(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=nan(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=nan(9,3);
[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);
temp(temp==0)=nan;
stat_mat(:,j2)=temp;
d=d+9;
end
p_sat=anova1(stat_mat);
close all
anova_sat{a_count,3}=p_sat;
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=nan(9,3);
[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);
temp(temp==0)=nan;
stat_mat(:,j2)=temp;
d=d+9;
end
p_chain=anova1(stat_mat);
close all
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=nan(9,3);
[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);
temp(temp==0)=nan;
stat_mat(:,j3)=temp;
d=d+9;
end
p_chain=anova1(stat_mat);
close all
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
[r3,c3]=size(plot_combo);
plot_combo=rot90(plot_combo);
plot_combo=flipud(plot_combo);
NAME=group{i};
bar (1:c3, plot_combo, 'stack');
hold on
combo_text=cell.empty;
for i3=1:r3
t=num2str(text_combo(i3,1));
v=num2str(text_combo(i3,2));
x=[v ':' t];
combo_text{i3}=x;
end
legend(combo_text, 'Location', 'EastOutside');
ylim([0 100]);
ylabel(['% of ' NAME ' with length:saturation']);
if T==6
set(gca, 'XTickLabel', {'8', '16', '24', '32', '40', '48'});
elseif T==3
set (gca, 'XTickLabel', {'Control', 'Early', 'Late'});
end
print (gcf, '-dpng', [label '_' NAME '_combo.png']);
print (gcf, '-depsc2', [label '_' NAME '_combo.eps']);
close
[r3,c3]=size(plot_length);
plot_length=rot90(plot_length);
plot_length=flipud(plot_length);
bar (1:c3, plot_length, 'stack');
hold on
length_plot=cell.empty;
for i3=1:r3
t=text_length(i3);
length_plot{i3}=num2str(t);
end
legend (length_plot, 'Location', 'EastOutside');
hold off
ylim([0 100]);
ylabel(['% of ' NAME ' with chain length']);
if T==6
set(gca, 'XTickLabel', {'8', '16', '24', '32', '40', '48'});
elseif T==3
set (gca, 'XTickLabel', {'Control', 'Early', 'Late'});
end
print (gcf, '-dpng', [label '_' NAME '_length.png']);
print (gcf, '-depsc2', [label '_' NAME '_length.eps']);
close
[r3,c3]=size(plot_sat);
plot_sat=rot90(plot_sat);
plot_sat=flipud(plot_sat);
bar (1:c3, plot_sat, 'stack');
hold on
length_sat=cell.empty;
for i3=1:r3
t=num2str(text_sat(i3));
length_sat{i3}=t;
end
legend (length_sat, 'Location', 'EastOutside');
ylim([0 100]);
ylabel(['% of ' NAME ' with saturation level']);
if T==6
set(gca, 'XTickLabel', {'8', '16', '24', '32', '40', '48'});
elseif T==3
set (gca, 'XTickLabel', {'Control', 'Early', 'Late'});
end
print (gcf, '-dpng', [label '_' NAME '_saturation.png']);
print (gcf, '-depsc2', [label '_' NAME '_saturation.eps']);
close
else %% if its the control---------------------------------------
for k2=1:r1
for j=1:6
time_mat(k2,j)=nanmean(levels(k2,1:3));
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;
for j=1:length(unique_sat)
u=unique_sat(j);
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=1:6
plot_sat(j,j2)=(lipid_sum(j2)/sum_(j2))*100;
end
text_sat(j)=u;
end
unique_length=unique(chain_length);
plot_length=zeros(length(unique_length),T);
for j=1:length(unique_length)
u=unique_length(j);
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=1:6
plot_length(j,j2)=(lipid_sum(j2)/sum_(j2))*100;
end
text_length(j)=u;
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=1:6
plot_combo(count,j3)=(lipid_sum(j3)/sum_(j3))*100;
end
text_combo(count,1)=us;
text_combo(count,2)=ul;
count=count+1;
end
end
end
subplot(1,3,1);
[r3,c3]=size(plot_combo);
plot_combo=rot90(plot_combo);
plot_combo=flipud(plot_combo);
NAME=group{i};
bar (1:2:c3*2, plot_combo, 'stack');
hold on
combo_text=cell.empty;
for i3=1:r3
t=num2str(text_combo(i3,1));
v=num2str(text_combo(i3,2));
x=[v ':' t];
combo_text{i3}=x;
end
legend(combo_text, 'Location', 'EastOutside');
ylim([0 100]);
xlim([0 2]);
ylabel(['% of ' NAME ' with length:saturation']);
if T==6
set(gca, 'XTickLabel', {'Control', '16', '24', '32', '40', '48'});
elseif T==3
set (gca, 'XTickLabel', {'Control', 'Early', 'Late'});
end
print (gcf, '-dpng', [label '_' NAME '_combo.png']);
print (gcf, '-depsc2', [label '_' NAME '_combo.eps']);
close
subplot(1,3,1);
[r3,c3]=size(plot_length);
plot_length=rot90(plot_length);
plot_length=flipud(plot_length);
bar (1:2:c3*2, plot_length, 'stack');
hold on
length_plot=cell.empty;
for i3=1:r3
t=num2str(text_length(i3));
length_plot{i3}=t;
end
legend (length_plot, 'Location', 'EastOutside');
hold off
ylim([0 100]);
ylabel(['% of ' NAME ' with chain length']);
if T==6
set(gca, 'XTickLabel', {'Control', '16', '24', '32', '40', '48'});
elseif T==3
set (gca, 'XTickLabel', {'Control', 'Early', 'Late'});
end
xlim([0 2]);
print (gcf, '-dpng', [label '_' NAME '_length.png']);
print (gcf, '-depsc2', [label '_' NAME '_length.eps']);
close
subplot(1,3,1);
[r3,c3]=size(plot_sat);
plot_sat=rot90(plot_sat);
plot_sat=flipud(plot_sat);
bar (1:2:c3*2, plot_sat, 'stack');
length_sat=cell.empty;
for i3=1:r3
t=num2str(text_sat(i3));
length_sat{i3}=t;
end
legend (length_sat, 'Location', 'EastOutside');
ylim([0 100]);
xlim([0 2]);
ylabel(['% of ' NAME ' with saturation level']);
if T==6
set(gca, 'XTickLabel', {'Control', '16', '24', '32', '40', '48'});
elseif T==3
set (gca, 'XTickLabel', {'Control', 'Early', 'Late'});
end
print (gcf, '-dpng', [label '_' NAME '_saturation.png']);
print (gcf, '-depsc2', [label '_' NAME '_saturation.eps']);
close
end
end
end