major backup update

clustergram/OR_clustergram_KVR_090213.m

@@ -0,0 +1,44 @@
+%make heatmaps out of the relative risk matrix 
+xlab={'2001', '2003', '2005', '2007', '2009', '2011'}; 
+
+indx2=find(strcmp(odds_ratio_cell(:,2),'Q32')~=1 & strcmp(odds_ratio_cell(:,2),'Q16')~=1  & strcmp(odds_ratio_cell(:,2),'Q53')~=1 & strcmp(odds_ratio_cell(:,2),'Q17')~=1 & strcmp(odds_ratio_cell(:,2),'Q22')~=1 & strcmp(odds_ratio_cell(:,2),'Q55')~=1 & strcmp(odds_ratio_cell(:,2),'Q56')~=1 & strcmp(odds_ratio_cell(:,2),'Q68')~=1 & strcmp(odds_ratio_cell(:,2),'Q69')~=1);
+odds_ratio_cell=odds_ratio_cell(indx2,:); 
+
+indx2=find(strcmp(odds_ratio_cell(:,1),'Q32')~=1 & strcmp(odds_ratio_cell(:,1),'Q16')~=1  & strcmp(odds_ratio_cell(:,1),'Q53')~=1 & strcmp(odds_ratio_cell(:,1),'Q17')~=1 & strcmp(odds_ratio_cell(:,1),'Q22')~=1 & strcmp(odds_ratio_cell(:,1),'Q55')~=1 & strcmp(odds_ratio_cell(:,1),'Q56')~=1 & strcmp(odds_ratio_cell(:,1),'Q68')~=1 & strcmp(odds_ratio_cell(:,1),'Q69')~=1);
+odds_ratio_cell=odds_ratio_cell(indx2,:); 
+
+for i=1 %1:70
+    i_char=num2str(i); 
+    q1_=i_char; 
+    num2=i; 
+    if (num2~=32 && num2~=16 && num2~=53 && num2~=17 && num2~=22 && num2~=55 && num2~=56 && num2~=68 && num2~=69);
+        if length(i_char)<2
+            i_char=['0' i_char]; 
+        end 
+        q1=['Q' i_char]; 
+        indx=find (strcmp(odds_ratio_cell(:,1),q1)==1); 
+        if isempty(indx)==0
+            plot_mat=cell2mat(odds_ratio_cell(indx,3:8)); 
+            q2=odds_ratio_cell(indx,2);
+            q2_=cell(length(q2),1); 
+            for p=1:length(q2)
+                s=q2{p,1}; 
+                q2_{p,1}=s(2:3); 
+            end 
+            indx2=find(isinf(plot_mat)==1); 
+            plot_mat(indx2)=-1; 
+            maxv=max(max(plot_mat)); 
+            plot_mat(indx2)=maxv;
+            log_rel_risk=log2(plot_mat); 
+            indx3=find(log_rel_risk<-100000); 
+            minv=min(min(log_rel_risk)); 
+            log_rel_risk(indx3)=minv; 
+            cg=clustergram(log_rel_risk,'RowLabels',q2_, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+            fig=plot(cg); 
+            tightfig; 
+            print (gcf,'-dmeta',[q1 '_clustermap_OR_090313.emf']); 
+            hm=HeatMap(log_rel_risk,'RowLabels',q2_, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+        end 
+    end 
+    close 
+end 

clustergram/OR_clustergram_KVR_090213_77.m

@@ -0,0 +1,52 @@
+%make heatmaps out of the relative risk matrix 
+xlab={'2009', '2011'}; 
+odds_ratio_cell=OR_cell; 
+
+indx2=find(strcmp(odds_ratio_cell(:,2),'Q32')~=1 & strcmp(odds_ratio_cell(:,2),'Q16')~=1  & strcmp(odds_ratio_cell(:,2),'Q53')~=1 & strcmp(odds_ratio_cell(:,2),'Q17')~=1 & strcmp(odds_ratio_cell(:,2),'Q22')~=1 & strcmp(odds_ratio_cell(:,2),'Q55')~=1 & strcmp(odds_ratio_cell(:,2),'Q56')~=1 & strcmp(odds_ratio_cell(:,2),'Q68')~=1 & strcmp(odds_ratio_cell(:,2),'Q69')~=1);
+odds_ratio_cell=odds_ratio_cell(indx2,:); 
+
+indx2=find(strcmp(odds_ratio_cell(:,1),'Q32')~=1 & strcmp(odds_ratio_cell(:,1),'Q16')~=1  & strcmp(odds_ratio_cell(:,1),'Q53')~=1 & strcmp(odds_ratio_cell(:,1),'Q17')~=1 & strcmp(odds_ratio_cell(:,1),'Q22')~=1 & strcmp(odds_ratio_cell(:,1),'Q55')~=1 & strcmp(odds_ratio_cell(:,1),'Q56')~=1 & strcmp(odds_ratio_cell(:,1),'Q68')~=1 & strcmp(odds_ratio_cell(:,1),'Q69')~=1);
+odds_ratio_cell=odds_ratio_cell(indx2,:); 
+
+for i=77
+    i_char=num2str(i); 
+    q1_=i_char; 
+    num2=i; 
+    if (num2~=32 && num2~=16 && num2~=53 && num2~=17 && num2~=22 && num2~=55 && num2~=56 && num2~=68 && num2~=69);
+        if length(i_char)<2
+            i_char=['0' i_char]; 
+        end 
+        q1=['Q' i_char]; 
+        indx=find (strcmp(odds_ratio_cell(:,1),q1)==1); 
+        if isempty(indx)==0
+            plot_mat=cell2mat(odds_ratio_cell(indx,3:4)); 
+            q2=odds_ratio_cell(indx,2);
+            q2_=cell(length(q2),1); 
+            for p=1:length(q2)
+                s=q2{p,1}; 
+                q2_{p,1}=s(2:3); 
+            end 
+            indx2=find(isinf(plot_mat)==1); 
+            plot_mat(indx2)=-1; 
+            maxv=max(max(plot_mat)); 
+            plot_mat(indx2)=maxv;
+            log_rel_risk=log2(plot_mat); 
+            indx3=find(log_rel_risk<-100000); 
+            minv=min(min(log_rel_risk)); 
+            log_rel_risk(indx3)=minv; 
+            %cg=clustergram(log_rel_risk,'RowLabels',q2_, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+            fig=plot(cg); 
+            tightfig; 
+           % print (gcf,'-dmeta',[q1 '_clustermap_OR_090313.emf']); 
+            %cg=clustergram(plot_mat,'RowLabels',q2_, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+            fig=plot(cg); 
+            tightfig; 
+            %print (gcf,'-dmeta',[q1 '_clustermap_OR_090313_nolog.emf']); 
+            hm=HeatMap(log_rel_risk,'RowLabels',q2_,'ColumnLabels',xlab,'ColorMap','jet'); 
+            %print (gcf, '-dmeta',[q1 '_heatmap_OR_090313.emf']); 
+            %hm=HeatMap(plot_mat,'RowLabels',q2_,'ColumnLabels',xlab,'ColorMap','jet'); 
+            %print (gcf, '-dmeta',[q1 '_heatmap_OR_090313_nolog.emf']); 
+        end 
+    end 
+    close 
+end 

clustergram/OR_clustergram_peryear.m

@@ -0,0 +1,44 @@
+%make heatmaps out of the relative risk matrix 
+years={'2001', '2003', '2005', '2007', '2009', '2011'}; 
+
+indx2=find(strcmp(odds_ratio_cell(:,2),'Q32')~=1 & strcmp(odds_ratio_cell(:,2),'Q16')~=1  & strcmp(odds_ratio_cell(:,2),'Q53')~=1 & strcmp(odds_ratio_cell(:,2),'Q17')~=1 & strcmp(odds_ratio_cell(:,2),'Q22')~=1 & strcmp(odds_ratio_cell(:,2),'Q55')~=1 & strcmp(odds_ratio_cell(:,2),'Q56')~=1 & strcmp(odds_ratio_cell(:,2),'Q68')~=1 & strcmp(odds_ratio_cell(:,2),'Q69')~=1);
+odds_ratio_cell=odds_ratio_cell(indx2,:); 
+
+indx2=find(strcmp(odds_ratio_cell(:,1),'Q32')~=1 & strcmp(odds_ratio_cell(:,1),'Q16')~=1  & strcmp(odds_ratio_cell(:,1),'Q53')~=1 & strcmp(odds_ratio_cell(:,1),'Q17')~=1 & strcmp(odds_ratio_cell(:,1),'Q22')~=1 & strcmp(odds_ratio_cell(:,1),'Q55')~=1 & strcmp(odds_ratio_cell(:,1),'Q56')~=1 & strcmp(odds_ratio_cell(:,1),'Q68')~=1 & strcmp(odds_ratio_cell(:,1),'Q69')~=1);
+odds_ratio_cell=odds_ratio_cell(indx2,:); 
+
+%remake cell for each year 
+q1=odds_ratio_cell(:,1); 
+q2=odds_ratio_cell(:,2);
+q_num=q2(1:52,1);
+xlab=q_num; 
+%rel_risk=zeros(66,66); 
+rel_risk=double.empty; 
+
+for j=6
+    for i=1:length(q_num)
+        q_char=(q_num{i}) ;
+        indx1=find(strcmp(q1(:),q_char)==1); 
+        n=1; 
+        for k=1:length(indx1)
+            indx=indx1(k); 
+            rel_risk(n,i)=odds_ratio_cell{indx,j+2}; 
+            n=n+1; 
+        end 
+    end 
+    rel_risk2=rel_risk; 
+    indx2=find(isinf(rel_risk2)==1); 
+    rel_risk2(indx2)=-1; 
+    maxv=max(max(rel_risk2)); 
+    rel_risk2(indx2)=maxv;
+    log_rel_risk=log2(rel_risk2); 
+    indx3=find(log_rel_risk<-100000); 
+    minv=min(min(log_rel_risk)); 
+    log_rel_risk(indx3)=minv; 
+    cg2=clustergram(log_rel_risk,'RowLabels', xlab, 'ColumnLabels',xlab, 'Colormap','jet'); 
+    fig2=plot(cg2); 
+    tightfig; 
+    print (gcf, '-dmeta', [years{j} '_clustergram_OR.emf']); 
+    hm=HeatMap(log_rel_risk,'RowLabels',xlab, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+    %close
+end 

clustergram/OR_clustergram_peryear_RC.m

@@ -0,0 +1,74 @@
+%make heatmaps out of the relative risk matrix 
+years={'2001', '2003', '2005', '2007', '2009', '2011'}; 
+cd ..
+cd ..
+cd matrices
+load relative_risk_RC_010414.mat 
+load q_labels_010414.mat
+load order.mat
+cd ..
+
+%remake cell for each year 
+q1=odds_ratio_cell(:,1); 
+q2=odds_ratio_cell(:,2);
+q_num=q2(1:56,1);
+xlab=q_num; 
+rel_risk=double.empty; 
+
+for j=6
+    for i=1:length(q_num)-1
+        q_char=(q_num{i}) ;
+        indx1=find(strcmp(q1(:),q_char)==1); 
+        n=1; 
+        for k=1:length(indx1)-1
+            indx=indx1(k); 
+            rel_risk(n,i)=odds_ratio_cell{indx,j+2}; 
+            n=n+1; 
+        end 
+    end 
+    [r,c]=size(rel_risk); 
+    rel_risk2=zeros(r,c);
+    qlabel2=cell(r,1); 
+    for i=1:length(order); 
+        in=order(i); 
+        rel_risk2(i,:)=rel_risk(in,:); %reorder by group
+        qlabel2(i,1)=qlabel(in,1); 
+    end  
+    rel_risk3=rel_risk2; 
+    rawOR=flipud(rel_risk3); 
+%     T=rel_risk2; 
+%     indx=find(isinf(T)==1); 
+%     T(indx)=-1; 
+%     maxv=max(max(T)); 
+%     rel_risk2(indx)=maxv; 
+    for i=1:r
+        temp_mat=rel_risk2(i,:); 
+        noinf=temp_mat; 
+        indx=find(isinf(noinf)==1); 
+        noinf(indx)=-1; 
+        maxv=max(noinf); 
+        temp_mat(indx)=maxv; 
+        rel_risk2(i,:)=temp_mat; 
+    end 
+    [r,c]=size(rel_risk2);
+    for i=1:r
+        med=median(rel_risk2(i,:)); 
+        rel_risk2(i,:)=rel_risk2(i,:)/med; 
+        %indx2=find(isinf(rel_risk2(:,i))==1); 
+        %rel_risk2(indx2,i)=maxv(i); 
+    end 
+    log_rel_risk=log2(rel_risk2);
+    normOR=flipud(log_rel_risk); 
+    for i=1:r
+        temp=log_rel_risk(i,:); 
+        minv=min(temp); 
+        indx3=find(log_rel_risk(i,:)<-100000); 
+        log_rel_risk(i,indx3)=minv; 
+    end 
+    %qqplot_figs(mat, [ years{j} '_log.png']); 
+    cg2=clustergram(log_rel_risk,'ColumnLabels',qlabel(:,1),'Cluster',2, 'Colormap','jet', 'DisplayRange',3); %'RowLabels',qlabel2(:,1),
+%     fig2=plot(cg2); 
+%     %tightfig;
+%     print (gcf, '-depsc2', [years{j} '_clustergram_OR']); 
+   % cg3=clustergram(rel_risk2, 'ColumnLabels',qlabel(:,1),'Cluster',2, 'Colormap','jet', 'DisplayRange',3, 'Symmetric','true');
+end 

clustergram/OR_clustergram_ques_RC.m

@@ -0,0 +1,72 @@
+%make heatmaps out of the relative risk matrix 
+
+cd .. 
+cd .. 
+cd matrices
+load rel_risk_RC_010414.mat
+load q_labels_010414.mat
+cd ..
+xlab={'2001', '2003', '2005', '2007', '2009', '2011'}; 
+
+ques=input ('Enter in the question number you want to use (ex. Q01): ', 's'); 
+for i=1:80
+    i_char=num2str(i); 
+    q1_=i_char; 
+    num2=i; 
+    if length(i_char)<2
+        i_char=['0' i_char]; 
+    end 
+    q1=['Q' i_char]; 
+    if strcmp(q1,ques)==1
+        indx=find (strcmp(odds_ratio_cell(:,1),q1)==1); 
+        if isempty(indx)==0
+            plot_mat=cell2mat(odds_ratio_cell(indx,3:8)); 
+            q2=odds_ratio_cell(indx,2);
+            q2_=cell(length(q2)-1,1); 
+            for p=1:length(q2)-1
+                s=q2{p,1}; 
+                q2_{p,1}=s(2:3); 
+            end  
+            plot_mat=plot_mat(1:56,:); 
+            plot_mat=rot90(plot_mat);
+            [r,c]=size(plot_mat); 
+            plot_mat2=plot_mat;
+            %qqplot_figs(plot_mat2, [ q1 '_raw']); 
+            for j=1:r
+                temp_mat=plot_mat(j,:); 
+                noinf=temp_mat; 
+                indx=find(isinf(noinf)==1); 
+                noinf(indx)=-1; 
+                maxv=max(noinf); 
+                temp_mat(indx)=maxv; 
+                plot_mat(j,:)=temp_mat; 
+            end
+            %median center
+            med=median(plot_mat,2); 
+            for j=1:r
+                med=median(plot_mat(j,:)); 
+                plot_mat(j,:)=plot_mat(j,:)/med; 
+            end 
+            log_rel_risk=log2(plot_mat); 
+            for j=1:r
+                temp=log_rel_risk(j,:); 
+                minv=min(temp); 
+                indx3=find(log_rel_risk(j,:)<-100000); 
+                log_rel_risk(j,indx3)=minv; 
+            end 
+            xlab=fliplr(xlab); 
+            %qqplot_figs(log_rel_risk, [ q1 '_log']); 
+            cg=clustergram(log_rel_risk,'RowLabels', xlab, 'ColumnLabels',qlabel(:,1),'Cluster',2, 'Colormap','jet', 'DisplayRange',3, 'Symmetric','true'); 
+            fig=plot(cg); 
+            tightfig; 
+            print (gcf,'-dpng',[q1 '_clustermap_OR_RC_LOG.png']); 
+            saveas(gcf,[q1 '_clustermap_OR_RC_LOG.fig']); 
+    %         cg=clustergram(plot_mat,'RowLabels',qlabel, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+    %         fig=plot(cg); 
+    %         tightfig; 
+    %         print (gcf,'-dmeta',[q1 '_clustermap_OR_RC.emf']);
+            %hm=HeatMap(log_rel_risk,'RowLabels',q2_, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+        end 
+        %close 
+    end 
+end 

clustergram/OR_clustergram_ques_RC_Q79.m

@@ -0,0 +1,68 @@
+%make heatmaps out of the relative risk matrix 
+
+cd matrices
+load OR_79_20
+load qlabel_031214
+cd ..
+xlab={ '2009', '2011'}; 
+odds_ratio_cell=OR_79; 
+ques='Q79'; 
+for i=1:80
+    i_char=num2str(i); 
+    q1_=i_char; 
+    num2=i; 
+    if length(i_char)<2
+        i_char=['0' i_char]; 
+    end 
+    q1=['Q' i_char]; 
+    if strcmp(q1,ques)==1
+        indx=find (strcmp(odds_ratio_cell(:,1),q1)==1); 
+        if isempty(indx)==0
+            plot_mat=cell2mat(odds_ratio_cell(indx,3:4)); 
+            q2=odds_ratio_cell(indx,2);
+            q2_=cell(length(q2)-1,1); 
+            for p=1:length(q2)-1
+                s=q2{p,1}; 
+                q2_{p,1}=s(2:3); 
+            end  
+            plot_mat=rot90(plot_mat);
+            [r,c]=size(plot_mat); 
+            plot_mat2=plot_mat;
+            %qqplot_figs(plot_mat2, [ q1 '_raw']); 
+            for j=1:r
+                temp_mat=plot_mat(j,:); 
+                noinf=temp_mat; 
+                indx=find(isinf(noinf)==1); 
+                noinf(indx)=-1; 
+                maxv=max(noinf); 
+                temp_mat(indx)=maxv; 
+                plot_mat(j,:)=temp_mat; 
+            end
+            %median center
+            med=median(plot_mat,2); 
+            for j=1:r
+                med=median(plot_mat(j,:)); 
+                plot_mat(j,:)=plot_mat(j,:)/med; 
+            end 
+            log_rel_risk=log2(plot_mat); 
+            for j=1:r
+                temp=log_rel_risk(j,:); 
+                minv=min(temp); 
+                indx3=find(log_rel_risk(j,:)<-100000); 
+                log_rel_risk(j,indx3)=minv; 
+            end 
+            xlab=fliplr(xlab); 
+            %qqplot_figs(log_rel_risk, [ q1 '_log']); 
+            cg=clustergram(log_rel_risk,'RowLabels', xlab, 'ColumnLabels',qlabel(:,1),'Cluster',2, 'Colormap','jet', 'DisplayRange',3, 'Symmetric','true'); 
+    %         fig=plot(cg); 
+    %         tightfig; 
+    %         print (gcf,'-dmeta',[q1 '_clustermap_OR_RC_LOG.emf']); 
+    %         cg=clustergram(plot_mat,'RowLabels',qlabel, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+    %         fig=plot(cg); 
+    %         tightfig; 
+    %         print (gcf,'-dmeta',[q1 '_clustermap_OR_RC.emf']);
+            %hm=HeatMap(log_rel_risk,'RowLabels',q2_, 'ColumnLabels', xlab, 'ColorMap', 'jet'); 
+        end 
+        %close 
+    end 
+end