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lipidomics_112313.m
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%create matrices from cell arrays DD2-------------
cd ..
cd matrices
load DD2_names.mat
load PFS_DD2.mat
load species.mat
cd ..
cd programs
DD2f=DD2fraction(4:307,2:109);
DD2f_parasite=cell2mat(DD2fraction(4:307,2:55));
DD2f_RBC=cell2mat(DD2fraction(4:307,56:109));
DD2f_p=reorder(DD2f_parasite);
DD2f_R=reorder(DD2f_RBC);
[DD2f_p_, mat_p_NaN]=filter_std(DD2f_p,9,6);
[DD2f_R_, mat_R_NaN]=filter_std(DD2f_R,9,6);
%uninfected RBC
uninfected=cell2mat(DD2fraction(4:307, 113:115));
[uninf, uinf_NaN]=filter_std(uninfected,3,1);
% %FIGURE 1- lipid species bar charts
% [mol_parasite, mol_rbc, mol_uninfected, plot_mat, mol_names1]=Figure1_v2( DD2f_p_, DD2f_R_, uninf, DD2f_names, species );
% [ anova_parasite, ttest_parasite, statdatap] = anova_ttest_final( DD2f_p_, DD2f_names, 6, 9 );
% [ anova_RBC, ttest_RBC, statdataR] = anova_ttest_final( DD2f_R_, DD2f_names, 6, 9 );
% [ pvalue_p_R, pvalue_p_u, pvalue_R_u ] = ttest_within_species( DD2f_p_, DD2f_R_, uninf, DD2f_names, 6);
%
% [anova_parasite_mol, ttest_parasite_mol, statdatatp_mol]=anova_ttest_final(mol_parasite, mol_names1, 6,9);
% [anova_RBC_mol, ttest_RBC_mol, statdataR_mol]=anova_ttest_final(mol_rbc, mol_names1, 6,9);
% [pvalue_p_R_mol, pvalue_p_u_mol, pvalue_R_u_mol]= ttest_within_species(mol_parasite, mol_rbc, mol_uninfected, mol_names1, 6);
%
cd ..
cd results
mkdir ('heatmaps')
cd ..
cd programs
%FIGURE 2 - heatmap
[ plot_mat_R, bar_mat_R, percent_changed_R, stats_R, names_R] = lipid_heatmap ( DD2f_R_, DD2f_names, 'RBC', species);
cmap='jet';
R=flipud(names_R);
H=HeatMap(R, 'Colormap', cmap, 'Symmetric','false' );
plot(H);
cd ..
cd results
cd heatmaps
print (gcf, '-dpng', 'RBC_names.png');
print (gcf, '-depsc2', ['RBC_names.eps']);
%saveas (gcf, 'RBC_names.fig');
cd ..
cd ..
cd programs
close all
[ plot_mat_p, bar_mat_p, percent_changed_p, stats_p, names_p ] = lipid_heatmap ( DD2f_p_, DD2f_names, 'parasite', species);
P=flipud(names_p);
H=HeatMap(P, 'Colormap', cmap, 'Symmetric','false');
plot(H);
cd ..
cd results
cd heatmaps
print (gcf, '-dpng', 'parasite_names.png')
print (gcf, '-depsc2', [ 'parasite_names.eps']);
%saveas (gcf, 'parasite_names.fig');
close all
cd ..
cd ..
cd programs
% %length and saturation bars
% [anova_sat_p, anova_chain_p, anova_combo_p, plot_combo_p, combo_text_p]= sat_length(DD2f_p_, DD2f_names, species, 'parasite', 6);
% [anova_sat_R, anova_chain_R, anova_combo_R, plot_combo_R, combo_text_R]= sat_length(DD2f_R_, DD2f_names, species, 'RBC', 6);
% [anova_sat_u, anova_chain_u, anova_combo_u, plot_combo_u, combo_text_u]=sat_length(uninf, DD2f_names, species, 'uninfected',1);
% [anova_sat_RC,anova_sat_PR,anova_sat_PC, anova_length_RC,anova_length_PR, anova_length_PC, anova_combo_RC,anova_combo_PR, anova_combo_PC] = sat_length_stats( uninf, DD2f_p_, DD2f_R_, DD2f_names, species );
%plot combo info
%plot_combo(plot_combo_p, plot_combo_R, plot_combo_u, combo_text_p);
% % %supernatant--------------------------------------------------
% cd ..
% cd matrices
% load super.mat
% load Supp_control.mat
% load super_names;
% cd ..
% cd programs
%
% super_mat=cell2mat(Supp_species(4:292,2:55));
% [super_, super_NaN]=filter_std(super_mat,9, 6);
% [super_cont, super_cont_NaN]=filter_std(control, 9, 2)
% [mol_super,mol_control, mol_uiRBC, plot_mat, mol_names]=Figure1_super( super_, control, super_names, species );
%[anova_super_mol, ttest_super_mol, statdatatS_mol]=anova_ttest_final(mol_super, mol_names, 6,9);
%[ pvalue_s_c, pvalue_s_u] = ttest_within_species_super(mol_super, mol_control, mol_uiRBC, mol_names, 6);
%[anova_super, ttest_super, statdata_super]=anova_ttest_final(super_, super_names, 6, 9);
% [plot_super, bar_mat_super, percent_super, stats_super, names_S]=lipid_heatmap(super_,super_names,'super', species);
% cmap='jet';
% S=flipud(names_S);
% H=HeatMap(S,'Colormap', cmap, 'Symmetric','false');
% plot(H);
% cd ..
% cd results
% cd heatmaps
% print (gcf, '-dpng', 'super_names.png')
% print (gcf, '-depsc2','super_names.eps');
% %saveas (gcf, 'super_names.fig')
% cd ..
% cd ..
% cd programs
% close all
%[anova_sat_S, anova_chain_S, anova_combo_S, plot_combo_S, combo_text_S]= sat_length(super_, super_names, species, 'super', 6);