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gametocytes_080214.m
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%used concentration values-----------------
cd ..
cd matrices
load gametocytes_update
load gam_controls
load species_v2
cd ..
cd programs
g_mat(:, 1:45)=gametocyte(:, 1:45);
g_mat(:, 46:54)=gametocyte(:, 49:57);
[G_mat, mat_G_NaN, N]=filter_std(g_mat,9,6);
l_malaria=G_mat(:,1:9);
l_infected=G_mat(:,10:18);
l_uninf=G_mat(:,19:27);
e_malaria=G_mat(:,28:36);
e_infected=G_mat(:,37:45);
e_uninf=G_mat(:,46:54);
late=G_mat(:,1:27);
early=G_mat(:,28:54);
late_NaN=mat_G_NaN(:,1:27);
early_NaN=mat_G_NaN(:,28:54);
[cont_mat,cont_mat_NaN,n1]=filter_std(gam_controls,3,1);
[ttest, plot_mat]=Figure1_gametocytes( early, late, gametocyte_text, species );
[ttest, plot_mat]=Figure1_gams_no_infected( early, late, gametocyte_text, species );
% [malaria_ttest, n3]= ttest_gametocyte( e_malaria, l_malaria, gametocyte_text, time4, time4_cell, time4_2, time4_2_cell);
% [infected_ttest, n4]=ttest_gametocyte( e_infected, l_infected, gametocyte_text, T4_mat, time4_cell, time4_2, time4_2_cell);
% [uninf_ttest, n5]=ttest_gametocyte(e_uninf, l_uninf, gametocyte_text, time4, time4_cell, time4_2, time4_2_cell);
%[early_ttest, n6]=ttest_gametocyte_compare2(e_infected, e_uninf, gametocyte_text);
%[late_ttest, n7]=ttest_gametocyte_compare2(l_infected, l_uninf, gametocyte_text);
% [early_ttest]=ttest_gametocyte2(e_malaria, e_infected, e_uninf, gametocyte_text);
% [late_ttest]=ttest_gametocyte2(l_malaria, l_infected, l_uninf, gametocyte_text);
%
% [malaria_ttest2]= ttest_gametocyte_trop1(e_malaria, l_malaria, gametocyte_text, T4_mat, time4_cell);
% [infected_ttest2]=ttest_gametocyte_trop1(e_infected, l_infected, gametocyte_text, T4_mat, time4_cell);
% [uninf_ttest2]=ttest_gametocyte_trop1(e_uninf, l_uninf, gametocyte_text, T4_mat, time4_cell);
% [r,c]=size(early);
% %heatmap
% [r_c,c_c]=size(gam_controls);
% [ plot_mat, stat_mat, stat_mat2] = gametocyte_heatmapv2( e_malaria(14:r,:), l_malaria(14:r,:), gametocyte_text(14:r,:), cont_mat(10:r_c,:), gam_controls_text(10:r_c,:), species);
% %[stat_mat, plot_mat]=Figure1_gametocytes( early, late, gametocyte_text, species );
%
% H=HeatMap(HM_names2, 'Colormap', cmap, 'Symmetric','false');
% [plot_mat, HM_names2]= gametocyte_heatmap_step2 ( e_malaria(14:r,:), l_malaria(14:r,:), gametocyte_text(14:r,:),time4, time4_cell,time4_2, time4_2_cell );
% H=HeatMap(HM_names2, 'Colormap', cmap, 'Symmetric','false');
% plot(H);
% cd ..
% cd results
% cd heatmaps
% print (gcf, '-dpng', 'gametocyte_names.png')
% print (gcf, '-depsc2', ['gametocyte_names.eps']);
% %saveas (gcf, 'parasite_names.fig');
% close all
% cd ..
% cd ..
% cd programs
%
% both=cat(2,early,late);
% [r,c]=size(both);
% both=both(14:r, :);
% g_names=gametocyte_text(14:r,:);
% gam_text=gametocyte_text(14:r,:);
%
%
% [r,c]=size(both);
% all=nan(r,63);
% all(:,10:63)=both;
%
% %make new control matrix ------------------------
% for j=1:r
% name=g_names{j,1};
% indx=find(strcmp(gam_controls_text(:,1),name)==1);
% if numel(indx)>0
% all(j,1:3)=cont_mat(indx,:);
% end
% end
%[anova_sat_G, anova_chain_G, anova_combo_G, plot_combo_S, combo_text_S]= sat_length_gams_simple(all, g_names, species, 'gams', 7);