Skip to content

Commit

Permalink
backup
Browse files Browse the repository at this point in the history
  • Loading branch information
@kruggles7
kruggles7 committed Jul 9, 2015
1 parent efd1762 commit f63a02a
Show file tree
Hide file tree
Showing 38 changed files with 8,993 additions and 31 deletions.
93 changes: 93 additions & 0 deletions clustergram/OR_clustergram_peryear_RC_2013.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,93 @@
%make heatmaps out of the relative risk matrix
years={'2001', '2003', '2005', '2007', '2009', '2011', '2013'};
cd ..
cd ..
cd matrices
load OR_2013_110314.mat
load qlabel_090914.mat
load order_090914.mat
cd ..
cd programs
cd clustergrams

%remake cell for each year
q1=odds_ratio_cell(:,1);
q2=odds_ratio_cell(:,2);
q_num=q2(1:64,1);
xlab=q_num;
rel_risk=double.empty;
xlab_=cell.empty;

for j=7
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);
if isempty(odds_ratio_cell{indx,j+2})==0
rel_risk(n,i)=odds_ratio_cell{indx,j+2};
end
n=n+1;
end
end
sum_column=sum(rel_risk);
indx_0=find(sum_column>0);
rel_risk_=rel_risk(indx_0, indx_0);
xlab_=xlab(indx_0);
qlabel_=qlabel(indx_0,:);

[r,c]=size(rel_risk_);
rel_risk2=zeros(r,c);
qlabel2=cell(r,1);
m=1;
for i=1:length(order);
in=find(strcmp(qlabel_(:,2),order{i})==1);
if numel(in)>0
rel_risk2(m,:)=rel_risk_(in,:); %reorder by group
qlabel2(m,1)=qlabel_(in,1);
m=m+1;
end
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);
%med=median(rel_risk_2,2);
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);
qlab=qlabel_(:,1);
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;
indx3=find(isinf(log_rel_risk(i,:))==1);
log_rel_risk(i,indx3)=maxv;
end
names=flipud(qlabel2);
cg2=clustergram(log_rel_risk,'ColumnLabels',qlab,'Cluster',2, 'Colormap','jet', 'DisplayRange',3);
fig2=plot(cg2);
set(gcf, 'Renderer', 'Painters');
print (gcf, '-depsc2', [years{j} '_clustergram_OR']);
saveas (gcf, [years{j} '_clustergram_OR.fig']);
end
94 changes: 94 additions & 0 deletions clustergram/OR_clustergram_peryear_RC_2013_subgroup.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,94 @@
%make heatmaps out of the relative risk matrix
lab='hispanic_girls';
years={'2001', '2003', '2005', '2007', '2009', '2011', '2013'};
cd ..
cd ..
cd matrices
load OR_2013_HISPANIC_GIRLS.mat
load qlabel_090914.mat
load order_090914.mat
cd ..
cd programs
cd clustergrams

%remake cell for each year
q1=odds_ratio_cell(:,1);
q2=odds_ratio_cell(:,2);
q_num=q2(1:64,1);
xlab=q_num;
rel_risk=double.empty;
xlab_=cell.empty;

for j=7
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);
if isempty(odds_ratio_cell{indx,j+2})==0
rel_risk(n,i)=odds_ratio_cell{indx,j+2};
end
n=n+1;
end
end
sum_column=sum(rel_risk);
indx_0=find(sum_column>0);
rel_risk_=rel_risk(indx_0, indx_0);
xlab_=xlab(indx_0);
qlabel_=qlabel(indx_0,:);

[r,c]=size(rel_risk_);
rel_risk2=zeros(r,c);
qlabel2=cell(r,1);
m=1;
for i=1:length(order);
in=find(strcmp(qlabel_(:,2),order{i})==1);
if numel(in)>0
rel_risk2(m,:)=rel_risk_(in,:); %reorder by group
qlabel2(m,1)=qlabel_(in,1);
m=m+1;
end
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);
%med=median(rel_risk_2,2);
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);
qlab=qlabel_(:,1);
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;
indx3=find(isinf(log_rel_risk(i,:))==1);
log_rel_risk(i,indx3)=maxv;
end
names=flipud(qlabel2);
cg2=clustergram(log_rel_risk,'ColumnLabels',qlab,'Cluster',2, 'Colormap','jet', 'DisplayRange',3);
fig2=plot(cg2);
set(gcf, 'Renderer', 'Painters');
print (gcf, '-dpdf', [years{j} '_clustergram_OR_' lab]);
saveas (gcf, [years{j} '_clustergram_OR_' lab '.fig']);
end
138 changes: 138 additions & 0 deletions clustergram/OR_clustergram_ques_RC_2013_all_questions.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,138 @@
%make heatmaps out of the relative risk matrix

cd ..
cd ..
cd matrices
load OR_2013_110314.mat
load qlabel_090914.mat
cd ..
cd programs
cd clustergrams
cd results
xlab={'2013', '2011', '2009', '2007', '2005', '2003', '2001'};

ques=input ('Enter in the question number you want to use (ex. Q01): ', 's');
for i=1:82
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
lab=odds_ratio_cell(indx,2);
P=odds_ratio_cell(indx,3:9);
P2=cell.empty;
qlabel2=cell.empty;
[rl,cl]=size(qlabel);
counter=1;
for j=1:rl
indx=find(strcmp(qlabel{j,2},lab)==1 & strcmp(lab, ques)==0);
if numel(indx)>0
P2(counter,:)=P(indx,:);
qlabel2(counter,:)=qlabel(j,:);
counter=counter+1;
end

end
%replace NaN with -10000
indx=find(strcmp(P2,'NaN')==1);
for j=1:numel(indx)
P2{indx(j)}=-10000;
end
indx=find(strcmp(P2,'Inf')==1);
for j=1:numel(indx)
P2{indx(j)}=10000;
end
emptycells=cellfun(@isempty, P2);
[r,c]=size(emptycells);
for j=1:r
for k=1:c
if (emptycells(j,k)==1)
P2{j,k}=-10000;
end
end
end
plot_mat=cell2mat(P2);
[r,c]=size(plot_mat);

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_mat(plot_mat==-10000)=NaN;
plot_mat3=plot_mat;
xlab_new=xlab;
qlab_new=qlabel2(:,1);
% %create second matrix without NaN
% plot_mat2=double.empty;
% xlab_new=cell.empty;
% counter=1;
% for j=1:r
% indx=find(isnan(plot_mat(j,:))==0) ;
% if isempty(indx)==0 %entire row is NOT nan
% plot_mat2(counter,:)=plot_mat(j,:);
% xlab_new{counter}=xlab{j};
% counter=counter+1;
% end
% end
% %remove questions that don't have all of the same years
% [r,c]=size(plot_mat2);
% plot_mat3=double.empty;
% qlab_new=cell.empty;
% counter=1;
% for j=1:c
% indx=find(isnan(plot_mat2(:,j))==1);
% if numel(indx)==0
% plot_mat3(:,counter)=plot_mat2(:,j);
% qlab_new{counter}=qlabel2{j,:};
% counter=counter+1;
% end
% end

%create 3rd matrix without the maximum values
[r,c]=size(plot_mat3);
plot_mat3(isinf(plot_mat3)==1)=-10000 ;
plot_mat3(plot_mat3==10000)=-10000;
for j=1:r
maxv=nanmax(plot_mat3(j,:));
indx_inf=find(plot_mat3(j,:)==-10000);
if numel(indx_inf)>0
plot_mat3(j,indx_inf)=maxv;
end
end
%median center
for j=1:r
med=nanmedian(plot_mat3(j,:));
plot_mat3(j,:)=plot_mat3(j,:)/med;
end
log_rel_risk=log2(plot_mat3);
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
for j=1:r
for k=1:c
if isnan(log_rel_risk(j,k))==1
log_rel_risk(j,k)=nanmean(log_rel_risk(:,k));
end
end
end
cg=clustergram(log_rel_risk,'RowLabels', xlab_new, 'ColumnLabels',qlab_new,'Cluster',2, 'Colormap','jet', 'DisplayRange',3, 'Symmetric','true');
fig=plot(cg);
%tightfig;
print (gcf,'-dpng',[q1 '_clustermap_OR_RC_2013.png']);
saveas(gcf,[q1 '_clustermap_OR_RC_2013.fig']);
end
%close
end
end
Loading

0 comments on commit f63a02a

Please sign in to comment.