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gametocyte_heatmapv2.m
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function [ plot_mat, stat_mat, stat_mat2 ] = gametocyte_heatmapv2( early, late, g_names, control ,c_names, species)
% [r,c]=size(early);
% early=e_malaria(14:r,:);
% late=l_malaria(14:r,:);
% g_names=gametocyte_text(14:r,:);
% control1=time4;
% control2=time4_2;
% c_names1=time4_cell;
% c_names2=time4_2_cell;
[r,c]=size(early);
c_mat=zeros(r,3);
%make new control matrix ------------------------
for j=1:r
name=g_names{j,1};
indx=find(strcmp(c_names(:,1),name)==1);
if numel(indx)>0
c_mat(j,1:3)=control(indx,:);
end
end
[r,c]=size(early);
sum_early=sum(early);
sum_late=sum(late);
sum_c=sum(c_mat);
mol_early=early;
mol_late=late;
mol_control=c_mat;
%foreach time
plot_mat=double.empty;
plot_total=zeros(1,21);
%for each experiment
for k=1:r
plot_total(1,1:3)=mol_control(k,1:3);
plot_total(1,4:12)=mol_early(k,1:9);
plot_total(1,13:21)=mol_late(k,1:9);
M=median(plot_total);
E=zeros(9,1);
L=zeros(9,1);
C=zeros(3,1);
for j=1:9
E(j)=mol_early(k,j)/M;
L(j)=mol_late(k,j)/M;
end
for j=1:3
C(j)=mol_control(k,j)/M;
end
plot_mat(k,1)=mean(C);
plot_mat(k,2)=mean(E);
plot_mat(k,3)=mean(L);
end
raw=plot_mat;
indx=find(plot_mat==0);
plot_mat(indx)=1;
indx=find(isnan(plot_mat)==1);
plot_mat(indx)=1;
plot_mat=log2(plot_mat);
x={'8','16','24','32','40','48'};
plots=flipud(plot_mat);
%G=flipud(G);
%name_group=names(:,1);
cmap=redgreencmap(256);
%cmap='jet';
x={'T4', 'early', 'late'};
%
H=HeatMap(plots,'ColumnLabels',x,'DisplayRange', 2, 'Colormap', cmap, 'Symmetric','true');
set(gca,'FontSize',16,'linewidth',2)
plot(H);
print (gcf, '-dpng', 'gametocyte_heatmap.png');
print (gcf, '-depsc2', 'gametocyte_heatmap.eps');
saveas(gcf, 'gametocyte_heatmap.fig');
%close
indx=find(isnan(plot_mat(:,1))==0 | isnan(plot_mat(:,2))==0 | isnan(plot_mat(:,3))==0);
plot_mat2=plot_mat(indx,:);
raw=raw(indx,:);
CONTROL=mol_control(indx,:);
EARLY=mol_early(indx,:);
LATE=mol_late(indx,:);
labels=g_names(indx,1);
indx=find(isnan(plot_mat2(:,1))==1);
indx2=find(isnan(plot_mat2(:,2))==1);
indx3=find(isnan(plot_mat2(:,3))==1);
plot_mat2(indx,1)=0;
plot_mat2(indx2,2)=0;
plot_mat2(indx3,3)=0;
[r,c]=size(raw);
%percent_changed=zeros(5,1);
group_percent=zeros(4,3);
group_percent_early=zeros(4,9);
group_percent_late=zeros(4,9);
group_total=zeros(4,1);
group_percent_early_late=zeros(4,9);
group_stats=zeros(4,3);
count=1;
for j=1:r
spec_num1=g_names{j,2};
spec_1=cell2mat(species(:,1));
indx=find(spec_1==spec_num1);
if numel(indx)==1
spec_num2=species(indx,3);
group=cell2mat(spec_num2) ;
error=0;
else
error=1;
end
if error==0 && group~=0
x1=raw(j,2);
x2=raw(j,1);
diff1=x1/x2;
if diff1>1.5 || diff1<0.66667
count=count+1;
group_percent(group,1)=group_percent(group,1)+1;
end
x1=raw(j,3);
x2=raw(j,1);
diff1=x1/x2 ;
group_total(group)=group_total(group)+1;
if diff1>1.5 || diff1<0.66667
count=count+1;
group_percent(group,2)=group_percent(group,2)+1;
end
x1=raw(j,2);
x2=raw(j,3);
diff1=x1/x2;
if diff1>1.5 || diff1<0.66667
count=count+1;
group_percent(group,3)=group_percent(group,3)+1;
end
%for each of the 9 samples
for b=1:9
x1=EARLY(j,b);
x2=LATE(j,b);
x3=mean(CONTROL(j,:));
diff1=x1/x3;
diff3=x2/x3;
if diff1>1.5 || diff1<0.6667
group_percent_early(group,b)=group_percent_early(group,b)+1;
end
if diff3>1.5 || diff3<0.6667
group_percent_late(group,b)=group_percent_late(group,b)+1;
end
diff2=x1/x2;
if diff2>1.5 || diff2<0.6667
group_percent_early_late(group,b)=group_percent_early_late(group,b)+1;
end
end
else
name;
end
end
bar_mat=zeros(4,3);
bar_error=zeros(4,3);
bar_mat2=zeros(4,1);
bar_error2=zeros(4,1);
bar_mat3=zeros(3,3);
bar_error3=zeros(3,3);
stat_mat=double.empty;
for j=1:4
ratio=group_percent_early(j,:)/group_total(j);
e_mean=mean(ratio);
e_std=std(ratio);
bar_mat(j,1)=e_mean;
bar_error(j,1)=e_std;
group_e=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
ratio=group_percent_late(j,:)/group_total(j) ;
l_mean=mean(ratio);
l_std=std(ratio);
bar_mat(j,2)=l_mean;
bar_error(j,2)=l_std;
group_l=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
ratio=group_percent_early_late(j,:)/group_total(j);
b_mean=mean(ratio);
b_std=std(ratio);
bar_mat(j,3)=b_mean;
bar_mat2(j,1)=b_mean;
bar_error(j,3)=b_std;
bar_error2(j,1)=b_std;
group_el=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
[h, stat_mat(j,1)]=ttest2(group_l, group_el);
[h, stat_mat(j,2)]=ttest2(group_e, group_el);
[h, stat_mat(j,3)]=ttest2(group_e, group_l);
end
stat_mat2=double.empty;
for j=1:3
if (j<3)
ratio=group_percent_early(j,:)/group_total(j);
e_mean=mean(ratio);
e_std=std(ratio);
bar_mat3(j,1)=e_mean;
bar_error3(j,1)=e_std;
group_e=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
ratio=group_percent_late(j,:)/group_total(j) ;
l_mean=mean(ratio);
l_std=std(ratio);
bar_mat3(j,2)=l_mean;
bar_error3(j,2)=l_std;
group_l=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
ratio=group_percent_early_late(j,:)/group_total(j);
b_mean=mean(ratio);
b_std=std(ratio);
bar_mat3(j,3)=b_mean;
bar_error3(j,3)=b_std;
group_el=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
[h, stat_mat2(j,1)]=ttest2(group_l, group_el);
[h, stat_mat2(j,2)]=ttest2(group_e, group_el);
[h, stat_mat2(j,3)]=ttest2(group_e, group_l);
else
ge=group_percent_early(3,:)+group_percent_early(4,:);
gt=group_total(3)+group_total(4);
gl=group_percent_late(3,:)+group_percent_late(4,:);
gel=group_percent_early_late(3,:)+group_percent_early_late(4,:);
ratio=ge/gt;
e_mean=mean(ratio);
e_std=std(ratio);
bar_mat3(j,1)=e_mean;
bar_error3(j,1)=e_std;
group_e=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
ratio=gl/gt ;
l_mean=mean(ratio);
l_std=std(ratio);
bar_mat3(j,2)=l_mean;
bar_error3(j,2)=l_std;
group_l=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
ratio=gel/gt;
b_mean=mean(ratio);
b_std=std(ratio);
bar_mat3(j,3)=b_mean;
bar_error3(j,3)=b_std;
group_el=[mean(ratio(1:3)) mean(ratio(4:6)) mean(ratio(7:9))];
[h, stat_mat2(j,1)]=ttest2(group_l, group_el);
[h, stat_mat2(j,2)]=ttest2(group_e, group_el);
[h, stat_mat2(j,3)]=ttest2(group_e, group_l);
end
end
% %%%TG and DG plots--------------------------------------------------
% %just early-late comparison
% bar_mat_=bar_mat2*-100;
% error_mat=bar_error2*100;
% bh=bar(bar_mat_, 1);
% bar_color=[-1 0.25 1 -0.35];
% ch=get(bh,'Children');
% set (ch,'CData',bar_color) ;
% colormap (gray);
% hold on
% errorbar (bar_mat_, error_mat, '.k', 'MarkerSize', 2);
% hold off
% colormap (gray);
% xlim([0 5]);
% %legend('PL', 'SL', 'NL', 'Location', 'SouthWest');
% set (gca, 'XTickLabel', {'PL', 'SL', 'TG', 'DG'});
% set (gca, 'YTick', [-100 -90 -80 -70 -60 -50 -40 -30 -20 -10 0]);
% set (gca, 'YTickLabel', [100 90 80 70 60 50 40 30 20 10 0]);
% ylabel('% of lipid class for species with >1.5X change');
% set(gca,'FontSize',16,'linewidth',2)
% print (gcf, '-dpng','gametocyte_heatmap_bars.png');
% print (gcf, '-depsc2', ['gametocyte_heatmap_bars.eps']);
% %saveas (gcf, 'gametocyte_heatmap_bars.fig');
% close all;
%
% %early-late-control comparison
% bar_mat_=bar_mat*-100;
% error_mat=bar_error*100;
% x=1:4;
% for j=1:3
% bar_mat_(:,j);
% bh=bar(x, bar_mat_(:,j), 1);
% ch=get(bh,'Children');
% set (ch,'CData',bar_color) ;
% colormap (gray);
% hold on
% errorbar (x, bar_mat_(:,j), error_mat (:,j), '.k', 'MarkerSize', 2);
% colormap (gray);
% x=x+[5 5 5 5] ;
% end
% hold off
% set(gca, 'XTick', [2.5, 7.5, 12.5]);
% set (gca, 'XTickLabel', {'early-control', 'late-control', 'early-late'});
% set (gca, 'YTick', [-100 -90 -80 -70 -60 -50 -40 -30 -20 -10 0]);
% set (gca, 'YTickLabel', [100 90 80 70 60 50 40 30 20 10 0]);
% set(gca,'FontSize',16,'linewidth',2)
% ylabel('% of lipid class for species with >1.5X change');
% print (gcf, '-dpng','gametocyte_heatmap_control_bars.png');
% print (gcf, '-depsc2', ['gametocyte_heatmap_control_bars.eps']);
% %saveas (gcf, 'gametocyte_heatmap_control_bars.fig');
%
% %NL plots----------------------------------------------
%
% %just early-late comparison
% %bar_mat_=bar_mat3(:,3)*-100 ;
% bar_mat_=bar_mat2(1:3,:)*-100;
% error_mat=bar_error2(1:3,:)*100;
% bh=bar(bar_mat_, 1);
% bar_color=[-1 0.25 1];
% ch=get(bh,'Children');
% set (ch,'CData',bar_color) ;
% colormap (gray);
% hold on
% errorbar (bar_mat_, error_mat, '.k', 'MarkerSize', 2);
% hold off
% colormap (gray);
% xlim([0 4]);
% set (gca, 'XTickLabel', {'PL', 'SL', 'NL'});
% set (gca, 'YTick', [-100 -90 -80 -70 -60 -50 -40 -30 -20 -10 0]);
% set (gca, 'YTickLabel', [100 90 80 70 60 50 40 30 20 10 0]);
% set(gca,'FontSize',16,'linewidth',2)
% ylabel('% of lipid class for species with >1.5X change');
% print (gcf, '-dpng','gametocyte_heatmap_bars_NL.png');
% print (gcf, '-depsc2', ['gametocyte_heatmap_bars_NL.eps']);
% %saveas (gcf, 'gametocyte_heatmap_bars_NL.fig');
% close all;
%
% %early-late-control comparison
% %bar_mat_=bar_mat3*-100;
% %error_mat=bar_error3*100;
% bar_mat_=bar_mat(1:3,:)*-100;
% error_mat=bar_error(1:3,:)*100;
% x=1:3;
% for j=1:3
% bh=bar(x, bar_mat_(:,j), 1);
% ch=get(bh,'Children');
% set (ch,'CData',bar_color) ;
% colormap (gray);
% hold on
% errorbar (x, bar_mat_(:,j), error_mat (:,j), '.k', 'MarkerSize', 2);
% colormap (gray);
% x=x+[4 4 4] ;
% end
% hold off
% set(gca, 'XTick', [1.5, 5.5, 9.5]);
% set (gca, 'XTickLabel', {'early-control', 'late-control', 'early-late'});
% set (gca, 'YTick', [-100 -90 -80 -70 -60 -50 -40 -30 -20 -10 0]);
% set (gca, 'YTickLabel', [100 90 80 70 60 50 40 30 20 10 0]);
% ylabel('% of lipid class for species with >1.5X change');
% set(gca,'FontSize',16,'linewidth',2)
% print (gcf, '-dpng','gametocyte_heatmap_control_bars_NL.png');
% print (gcf, '-depsc2', 'gametocyte_heatmap_control_bars_NL.eps');
% %saveas (gcf, 'gametocyte_heatmap_control_bars_NL.fig');
end