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BigPlot_cross_section_columns.m
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BigPlot_cross_section_columns.m
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%
% clear all
%
% dt_path_wt={ '../data/Nuclei_and_Cells_DT_S18_m6_wt/', '../data/Nuclei_and_Cells_DT_S17_m2_wt/',...
% '../data/Nuclei_and_Cells_DT_S84_m3_wt/', '../data/Nuclei_and_Cells_DT_S51_m2_wt/',...
% '../data/Nuclei_and_Cells_DT_S84_m4_wt/'};
%
% pt_path_wt = { '../data/Nuclei_and_Cells_PT_S18_m6_wt/','../data/Nuclei_and_Cells_PT_S17_m2_wt/',...
% '../data/Nuclei_and_Cells_PT_S84_m3_wt/','../data/Nuclei_and_Cells_PT_S51_m2_wt/',...
% '../data/Nuclei_and_Cells_PT_S84_m4_wt/'};
%
% dt_path_mut= {'../data/Nuclei_and_Cells_DT_S17_m1_mut/', '../data/Nuclei_and_Cells_DT_S18_m2_mut/' ,...
% '../data/Nuclei_and_Cells_DT_S84_m1_mut/', '../data/Nuclei_and_Cells_DT_S84_m5_mut/'};
%
% pt_path_mut = {'../data/Nuclei_and_Cells_PT_S17_m1_mut/', '../data/Nuclei_and_Cells_PT_S18_m2_mut/',...
% '../data/Nuclei_and_Cells_PT_S84_m1_mut/', '../data/Nuclei_and_Cells_PT_S84_m5_mut/', };
%
% du_path_wt={'../data/Nuclei_and_Cells_DU_S51_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m3_wt/'};
%
%
% allpath={dt_path_wt; pt_path_wt; dt_path_mut; pt_path_mut; du_path_wt};
%
%
% meanOfAllCelltemp=load('meanOfAllCell.dat');
% count=1;
% for gi=1:length(allpath)
% for gj=1:length(allpath{gi})
% %GlobalCenter{gi}{gj}=meanOfAllCelltemp(count,1:3);
% GlobalCenter{gi}{gj}=meanOfAllCelltemp(count,[6,9]);
% count=count+1;
% end
% end
%
%
%
% for gi=1:length(allpath)
% bonetype=gi;
% for gj=1:length(allpath{gi})
% path=allpath{gi}{gj};
% s=strsplit(path,'Nuclei_and_Cells_');
% input2=strcat('Columnar_Structure_Prediction_8_100/',s{2});
%
% pureColumn=load(['degree_of_the_column/StraightLine/pureColum_',s{2}(1:strlength(s{2})-1),'.dat']);
% column_curvature=load(['Curvature/Column_curvature_',s{2}(1:strlength(s{2})-1),'.mat']) ;
% ROC=load(['RadiusOfCurvature/ROC_',s{2}(1:strlength(s{2})-1),'.dat']);
%
%
% a1=load(['./../../',path,'all_cells_nuclei.mat']);
% nuc=a1.all_cells_nuclei;
% nuccent=nuc(:,5:7);
%
% C=mean(nuccent); %zgap=max(nuccent(:,3))-min(nuccent(:,3));
%
% limit=GlobalCenter{gi}{gj};
% starting=limit(1)+ 0.2*(limit(2)-limit(1));
% finishing=limit(1)+ 0.6*(limit(2)-limit(1));
% [limit,starting,finishing];
%
%
%
% nuccent1=nuccent-C;
% fixzmin=starting; fixzmax=finishing;
% if (bonetype==3)|(bonetype==1)
% zmin=-fixzmin; zmax=-fixzmax;
% colzmin=fixzmin;colzmax=fixzmax;
% else
% zmin=fixzmin; zmax=fixzmax; %70 add
% colzmin=zmin; colzmax=zmax;
% end
%
% shp = alphaShape(nuccent1);
% [tetrahedron,V] = alphaTriangulation(shp);
% trep = triangulation(tetrahedron, V);
% [tri, V] = freeBoundary(trep);
%
% if zmin<zmax
% PZboundary=find(V(:,3)>zmin & V(:,3)<zmax);
% nuc_PZ_boundary=find(nuccent1(:,3)>zmin & nuccent1(:,3)<zmax);
% else
% PZboundary=find(V(:,3)<zmin & V(:,3)>zmax);
% nuc_PZ_boundary=find(nuccent1(:,3)<zmin & nuccent1(:,3)>zmax);
% end
%
% x=V(PZboundary,1); y=V(PZboundary,2);
% K=boundary(x,y);
% databoundary{gi}{gj}=[x(K),y(K)];
%
%
% index=1;
% inverseR=[];
% for i=1:length(pureColumn)
% for j=1:length(ROC)
% if pureColumn(i)==ROC(j,1)
% if ROC(j,2)>=3
% if ((starting<=ROC(j,5)) & (ROC(j,6)<=finishing))
% inverseR=[inverseR;ROC(j,3:4)];
% twocell{index,1}=column_curvature.CurvatureOfColumn.NormalizedColumnCentroid{pureColumn(i)};
% index=index+1;
% end
% end
% end
% end
% end
%
%
%
%
% curvatureColormap{gi}{gj}=inverseR(:,1);
% nucleiDensity{gi}{gj}=nuccent1( nuc_PZ_boundary,1:2);
% data{gi}{gj}=twocell;
% %slope{gi}{gj}=sampleSlope;
% clear twocell
% %clear sampleSlope
% [size(data{gi}{gj},1), size( curvatureColormap{gi}{gj},1) ];
% end
% end
name{2}={ 'S18 m6','S17 m2', 'S84 m3', 'S51 m2', 'S84 m4' };
name{1}={ 'S18 m6','S17 m2', 'S84 m3', 'S51 m2', 'S84 m4' };
name{3}={ 'S17 m1', 'S18 m2', 'S84 m1', 'S84 m5' };
name{4}={ 'S17 m1', 'S18 m2', 'S84 m1', 'S84 m5' };
name{5}={ 'S51 m2', 'S84 m2', 'S84 m3'};
tname{5}='DU WT'; tname{4}='PT MT'; tname{3}='DT MT'; tname{2}='PT WT'; tname{1}='DT WT';
mycolor={'r','b','k','c','g'};
h1=figure();
XL=0.07;XR=0.03;XGap=0.02;Row=5;
YT=0.06;YB=0.08;YGap=0.05;Col=5;
Width=(1-XL-XR-((Col-1)*XGap))/Col;
Height=(1-YT-YB-((Row-1)*YGap))/Row;
YPos=1-YT-Height;
set(gcf, 'PaperSize', [15 12]);
set(gcf, 'PaperPosition', [0 0 15 12]);
U=[1,0,0]; mymap=colormap(redbluecmap(3));
map3=[0 0 1; 0 1 0; 1 0 0];
map2=[0 0 1; 0 1 0];
map4=[0 0 1; 0 1 0; 1 0 0;1 1 0];
map5=[0 0 1; 0 1 0; 1 0 0;1 1 0;1 0 1];
curvatureRange=linspace(0,200,50);
count=1;
for i=1:Row
XPos=XL;
for j=1:Col
chro=j+(i-1)*Col;
marray=[XPos,YPos,Width,Height];
if j<=length(data{i})
subplot('Position',marray);
column_coordinate=data{i}{j};
pzboundary=databoundary{i}{j};
nuclei=nucleiDensity{i}{j};
curvatureValue=curvatureColormap{i}{j};
mudata=[];
%[i,j,size(yr)]
for k=1:size(column_coordinate,1)
PC=pca(column_coordinate{k});
GC=mean(column_coordinate{k});
V=column_coordinate{k};
mudata(k,:)=GC(1:2);
colLen(k,1)=size(column_coordinate{k},1);
end
C=mean(nuclei);
%pzboundary=pzboundary-C;
goodmin=min(pzboundary);
goodmax=max(pzboundary);
if size(mudata,1)>1
%mudata=mudata-C;
goodindex=find((mudata(:,1)>goodmin(1))&(mudata(:,1)<goodmax(1))&(mudata(:,2)>goodmin(2))&(mudata(:,2)<goodmax(2)));
curvatureValue=curvatureValue(goodindex,:);
colLen= colLen(goodindex,:);
[th,r]=cart2pol(mudata(goodindex,1),mudata(goodindex,2));
ankit(count,:)=[min(curvatureValue), max(curvatureValue), length(unique(colLen))]; count=count+1;
sizeIndex=zeros(size(curvatureValue));
for k=2:length(curvatureRange)
allInd=find((curvatureValue>curvatureRange(k-1)) & (curvatureValue<=curvatureRange(k) ) );
sizeIndex(allInd,1)=curvatureRange(k);
end
polarscatter(th,r,10*sizeIndex, colLen ,'marker','.');
number= length(unique(colLen));
cbh=colorbar;
if number==2
cbr=colormap(gca,map2);
elseif number==3
cbr=colormap(gca,map3);
elseif number==4
cbr=colormap(gca,map4);
else
cbr=colormap(gca,map5);
end
cbh.Ticks=unique(colLen');
%slope=atan2(mudata(:,2),mudata(:,1));
%polarhistogram(slope,12,'FaceColor','b','normalization','probability','FaceAlpha',.3);
hold on
end
[th,r]=cart2pol(pzboundary(:,1),pzboundary(:,2));
polarplot(th,r,'color','m','marker','.','linestyle','-','linewidth',1);
%xr=[yr(:,1:3);yr(:,4:6)];
set(gca,'fontsize',7);
%[i,j,max(ankit(:,1)),min(ankit(:,1))];
%dlmwrite(['GlobalXangle/cosine_ratio_',num2str(i),'_',num2str(j),'.dat'],ankit,'\t');
%[i,j,100*sum(ankit>75)/length(ankit),100*sum(ankit<15)/length(ankit)];
%clear ankit
%axis([min(xr(:,1)),max(xr(:,1)),min(xr(:,2)),max(xr(:,2))])
%axis([-400,400,-400,400])
title(strcat(tname{i}, '-',name{i}{j}),'fontweight','normal','fontsize',7)
%legend(p,name{chro},'location','northwest');
end
XPos=XPos+Width+XGap;
end
YPos=YPos-YGap-Height;
end
saveas(h1,['column_cs_spatial_.png']);
%print(gcf,'Cross_section_50-250_mu','-dpdf','-r300');
function [xrange,yrange]=make_hist(x)
interval=[0:10:100];% [0:2:20,25:5:95];
y=zeros(1,length(interval)-1);
for i=2:length(interval)
y(i-1)=sum(find((x<interval(i)) & (x>=interval(i-1))));
end
yrange=(y/sum(y))';
xrange=(interval(1:end-1))';
end
function chooseColor=pickcolor(value,map)
colormap(map);
%map=(colormap(jet(6)));
theta=[0,15,30,45,60,75,90];
%theta=linspace(0,90,7);
%theta=[0,5,10,15,20,25,30,45,60,75,90];
for i=2:length(theta)
if value<=theta(i)
chooseColor=map(i-1,:);
break
end
end
end