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Copy pathBigPlot_straight_columns_orientation_with_CurveLine.m
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BigPlot_straight_columns_orientation_with_CurveLine.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};
for gi=1:length(allpath)
bonetype=gi;
for gj=1:length(allpath{gi})
path=allpath{gi}{gj};
s=strsplit(path,'Nuclei_and_Cells_');
%ns=strsplit(path,'T_');
%input2=strcat('Columnar_Structure_Prediction_8_100/',s{2});
%input1=strcat('MakeListColumnarStructurePrediction/',s{2});
column_curvature=load(['Curvature/Column_curvature_',s{2}(1:strlength(s{2})-1),'.mat']) ;
bone_curvature=load(['Curvature/CurvLine_',s{2}(1:strlength(s{2})-1),'.dat']);
pureColumn=load(['degree_of_the_column/StraightLine/pureColum_',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));
nuccent1=nuccent-C;
fixzmin=50; fixzmax=250;
if (bonetype==3)|(bonetype==1)
zmin=-fixzmin; zmax=-fixzmax;
colzmin=fixzmin;colzmax=fixzmax;
else
zmin=fixzmin+70; zmax=fixzmax+70;
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)];
for cutoff=[3,4,5]
output=findSlopeOfColumn(bone_curvature, column_curvature.CurvatureOfColumn,pureColumn,cutoff);
dataslope{gi}{gj}{cutoff}=output.sampleSlope;
data{gi}{gj}{cutoff}=output.twocell;
end
nucleiDensity{gi}{gj}=nuccent1( nuc_PZ_boundary,1:2);
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={'','','m','k','g','r','y'};
h1=figure();
XL=0.02;XR=0.03;XGap=0.02;Row=4;
YT=0.06;YB=0.03;YGap=0.07;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', [19.2 14.4]);
set(gcf, 'PaperPosition', [0 0 19.2 14.4]);
U=[1,0,0]; mymap=colormap(redbluecmap(6));
map=(colormap(jet(6)));
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);
pzboundary=databoundary{i}{j};
nuclei=nucleiDensity{i}{j};
for cutoff=3
slope=dataslope{i}{j}{cutoff};
column_coordinate=data{i}{j}{cutoff};
mudata=[];
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);
end
C=mean(nuclei);
pzboundary=pzboundary-C;
bmin=min(pzboundary);
bmax=max(pzboundary);
[thb,rb]=cart2pol(pzboundary(:,1),pzboundary(:,2));
if size(mudata,1)>1
mudata=mudata-C;
correctIndex=find( (mudata(:,1)>bmin(1))&(mudata(:,1)<bmax(1))&(mudata(:,2)>bmin(2))&(mudata(:,2)<bmax(2)));
[th,r]=cart2pol(mudata(correctIndex,1),mudata(correctIndex,2));
slope=slope(correctIndex,1);
clear myslope
myslope=[];
for p=1:length(slope)
myslope(p)=slope(p);
if slope(p)>90
myslope(p)=180-slope(p);
end
end
if length(myslope)>0
[int,orient]=avgOrientation(th,myslope);
statistical_test{i}{j}=[int(1:end-1)', orient(1:end-1)'];
polarplot(int,orient,'color',mycolor{cutoff},'marker','.','linestyle','-');
end
hold on
end
set(gca,'fontsize',7);
end
title(strcat(tname{i}, '-',name{i}{j}),'fontweight','normal','fontsize',7)
end
XPos=XPos+Width+XGap;
end
YPos=YPos-YGap-Height;
end
saveas(h1,['column_cs_mean_orient_curv_3.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
function [int,y]=avgOrientation(th,myslope)
interval=linspace(-pi-0.001,pi+0.001,13);
%interval=[interval,interval(end)+interval(2)-interval(1)];
for j=1:length(interval)-1
x=[];
for i=1:length(th)
if ((th(i)>interval(j)) & (th(i) <interval(j+1)))
x=[x,myslope(i)];
end
end
if length(x)==0
y(j)=0;
else
y(j)=mean(x);
end
int(j)=mean([interval(j),interval(j+1)]);
end
int(j+1)=int(1);
y(j+1)=y(1);
end