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Plot_DotComps.m
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Plot_DotComps.m
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%% Plot_DotComps.m %%
%
% Analyzing New Shadow data
%
%
% Alistair Boettiger Date Begun: 03/05/10
% Levine Lab Functional Since: 03/06/10
% Last Modified: 03/17/10
%% Description
% comparison
%
%
%% Updates
%% Source Code
clear all;
folder = '/Volumes/Data/Lab Data/Shadow_data';
s29_root = 'sogSxYW_29C_LacZ_sog';
sp29_root = 'sog2enh_29C_LacZ_sog';
sp22_root = 'sog2enh_22C_LacZ_sog';
s22_root = 'sogSxYW_22C_LacZ_sog';
p22_root = 'sogPxYW_22C_LacZ_sog';
p29_root = 'SogP30C_LacZ_sog';
N = 40;
p29_miss_cnt = zeros(N,1);
p29_miss_rate = zeros(N,1);
p29_lowon = zeros(N,1);
p22_miss_cnt = zeros(N,1);
p22_miss_rate = zeros(N,1);
p22_lowon = zeros(N,1);
s29_miss_cnt = zeros(N,1);
s29_miss_rate = zeros(N,1);
s29_lowon = zeros(N,1);
sp29_miss_cnt = zeros(N,1);
sp29_miss_rate = zeros(N,1);
sp29_lowon = zeros(N,1);
sp22_miss_cnt = zeros(N,1);
sp22_miss_rate = zeros(N,1);
sp22_lowon = zeros(N,1);
s22_miss_cnt = zeros(N,1);
s22_miss_rate = zeros(N,1);
s22_lowon = zeros(N,1);
for n=1:N
if n<10
emb = ['0',num2str(n)];
else
emb = num2str(n);
end
try
load([folder,'/',s29_root,emb,'_data.mat']);
% get the indices of all nuclei in green that are not also red.
% require these nuclei also fall in the 'region' for red nuclei.
s29_miss_cnt(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
s29_miss_rate(n) = s29_miss_cnt(n)/length(pts2);
s29_lowon(n) = lowon_fxn(H,handles,nin2);
catch ME
disp(['can not find file' folder,'/',s29_root,emb,'_data.mat']);
end
try
load([folder,'/',sp29_root,emb,'_data.mat']);
sp29_miss_cnt(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
sp29_miss_rate(n) = sp29_miss_cnt(n)/length(pts2);
sp29_lowon(n) = lowon_fxn(H,handles,nin2);
catch ME
disp(['can not find file' folder,'/',sp29_root,emb,'_data.mat']);
end
try
load([folder,'/',sp22_root,emb,'_data.mat']);
sp22_miss_cnt(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
sp22_miss_rate(n) = sp22_miss_cnt(n)/length(pts2);
sp22_lowon(n) = lowon_fxn(H,handles,nin2);
catch ME
disp(['can not find file' folder,'/',sp22_root,emb,'_data.mat']);
end
try
load([folder,'/',s22_root,emb,'_data.mat']);
s22_miss_cnt(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
s22_miss_rate(n) = sp22_miss_cnt(n)/length(pts2);
s22_lowon(n) = lowon_fxn(H,handles,nin2);
catch ME
disp(['can not find file' folder,'/',s22_root,emb,'_data.mat']);
end
try
load([folder,'/',p22_root,emb,'_data.mat']);
p22_miss_cnt(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
p22_miss_rate(n) = p22_miss_cnt(n)/length(pts2);
p22_lowon(n) = lowon_fxn(H,handles,nin2);
catch ME
disp(['can not find file' folder,'/',p22_root,emb,'_data.mat']);
end
try
load([folder,'/',p29_root,emb,'_data.mat']);
p29_miss_cnt(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
p29_miss_rate(n) = p29_miss_cnt(n)/length(pts2);
p29_lowon(n) = lowon_fxn(H,handles,nin2);
catch ME
disp(['can not find file' folder,'/',p29_root,emb,'_data.mat']);
end
end
save sog_shadow_data1
%%
load sog_shadow_data1;
x = linspace(0,1,40);
figure(3); clf; subplot(6,1,1); set(gcf,'color','w');
hist(nonzeros(sp29_lowon),x); legend('control 29C');
set(gca,'FontSize',15); xlim([0,max(x)]); ylabel('embryos'); xlabel('variation in total mRNA');
subplot(6,1,2); hist(nonzeros(s29_lowon),x); legend('no primary 29C');
set(gca,'FontSize',15); xlim([0,max(x)]); ylabel('embryos'); xlabel('variation in total mRNA');
subplot(6,1,3); hist(nonzeros(sp22_lowon),x); legend('control 22C');
set(gca,'FontSize',15); xlim([0,max(x)]); ylabel('embryos'); xlabel('variation in total mRNA');
subplot(6,1,4); hist(nonzeros(s22_lowon),x); legend('no primary 22C');
set(gca,'FontSize',15); xlim([0,max(x)]); ylabel('embryos'); xlabel('variation in total mRNA');
subplot(6,1,5); hist(nonzeros(p22_lowon),x); legend('no shadow 22C');
set(gca,'FontSize',15); xlim([0,max(x)]); ylabel('embryos'); xlabel('variation in total mRNA');
subplot(6,1,6); hist(nonzeros(p29_lowon),x); legend('no shadow 29C');
set(gca,'FontSize',15); xlim([0,max(x)]); ylabel('embryos'); xlabel('variation in total mRNA');
sp29_var = hist(nonzeros(sp29_lowon),x);
s29_var = hist(nonzeros(s29_lowon),x);
sp22_var = hist(nonzeros(sp22_lowon),x);
s22_var = hist(nonzeros(s22_lowon),x);
p29_var = hist(nonzeros(p29_lowon),x);
p22_var = hist(nonzeros(p22_lowon),x);
xx = linspace(0,1,100);
method = 'pcubic';
sigma = .1;
sp29_var_n = hist2dist(sp29_var,x,xx,method,sigma);
s29_var_n = hist2dist(s29_var,x,xx,method,sigma);
sp22_var_n = hist2dist(sp22_var,x,xx,method,sigma);
s22_var_n = hist2dist(s22_var,x,xx,method,sigma);
p29_var_n = hist2dist(p29_var,x,xx,method,sigma);
p22_var_n = hist2dist(p22_var,x,xx,method,sigma);
figure(2); clf;
C = hsv(6);
plot(xx,sp29_var_n,'color',C(1,:),'LineWidth',3); hold on;
plot(xx,s29_var_n,'color',C(2,:),'LineWidth',3);
plot(xx,sp22_var_n,'color',C(3,:),'LineWidth',3);
plot(xx,s22_var_n,'color',C(4,:),'LineWidth',3);
plot(xx,p29_var_n,'color',C(5,:),'LineWidth',3);
plot(xx,p22_var_n,'color',C(6,:),'LineWidth',3);
legend('2-enh 29C','no primary 29C','2-enh 22C','no primary 22C',...
'no shadow 29C', 'no shadow 22C');
set(gcf,'color','w'); set(gca,'FontSize',15);
xlabel('variance of transcript intensity');
xlim([0,.7]);
V{1} = nonzeros(sp29_lowon);
V{2} = nonzeros(s29_lowon);
V{3} = nonzeros(sp22_lowon);
V{4} = nonzeros(s22_lowon);
V{5} = nonzeros(p29_lowon);
V{6} = nonzeros(p22_lowon);
P_var = zeros(6,6);
for i=1:6
for j=1:6
P_var(i,j) = log10(ranksum(V{i},V{j}));
end
end
gn = {'2-enh 29C','no primary 29C','2-enh 22C','no primary 22C',...
'no shadow 29C', 'no shadow 22C'};
figure(6); clf; imagesc(P_var); colorbar; colormap('cool');
set(gca,'YtickLabel', str2mat(gn{:}),'YTick',1:6,'fontsize',15,...
'YMinorTick','on'); title('Variance in Total mRNA');
%%
x = linspace(0,1,13);
figure(1); clf; subplot(6,1,1); set(gcf,'color','w');
hist(nonzeros(sp29_miss_rate),x);title('control 29C','FontSize',15);% legend('control 29C');
set(gca,'FontSize',15); xlim([0,1]); ylabel('embryos'); xlabel('fraction missing nuclei');
subplot(6,1,2); hist(nonzeros(s29_miss_rate),x); title('no primary 29C','FontSize',15); % legend('no primary 29C');
set(gca,'FontSize',15); xlim([0,1]); ylabel('embryos'); xlabel('fraction missing nuclei');
subplot(6,1,3); hist(nonzeros(sp22_miss_rate),x); title('control 22C','FontSize',15); % legend('control 22C');
set(gca,'FontSize',15); xlim([0,1]); ylabel('embryos'); xlabel('fraction missing nuclei');
subplot(6,1,4); hist(nonzeros(s22_miss_rate),x); title('no primary 22C','FontSize',15);% legend('no primary 22C');
set(gca,'FontSize',15); xlim([0,1]); ylabel('embryos'); xlabel('fraction missing nuclei');
subplot(6,1,5); hist(nonzeros(p22_miss_rate),x); title('no shadow 22C','FontSize',15);% legend('no primary 22C');
set(gca,'FontSize',15); xlim([0,1]); ylabel('embryos'); xlabel('fraction missing nuclei');
subplot(6,1,6); hist(nonzeros(p29_miss_rate),x); title('no shadow 29C','FontSize',15);% legend('no primary 22C');
set(gca,'FontSize',15); xlim([0,1]); ylabel('embryos'); xlabel('fraction missing nuclei');
sp29_miss = hist(nonzeros(sp29_miss_rate),x);
s29_miss = hist(nonzeros(s29_miss_rate),x);
sp22_miss = hist(nonzeros(sp22_miss_rate),x);
s22_miss = hist(nonzeros(s22_miss_rate),x);
xx = linspace(0,1,100);
method = 'pcubic';
sigma = .15;
sp29_miss = hist2dist(sp29_miss,x,xx,method,sigma);
s29_miss = hist2dist(s29_miss,x,xx,method,sigma);
sp22_miss = hist2dist(sp22_miss,x,xx,method,sigma);
s22_miss = hist2dist(s22_miss,x,xx,method,sigma);
figure(4); clf; set(gcf,'color','w');
C = hsv(4);
plot(xx,sp29_miss,'color',C(1,:),'LineWidth',3); hold on;
plot(xx,s29_miss,'color',C(2,:),'LineWidth',3);
plot(xx,sp22_miss,'color',C(3,:),'LineWidth',3);
plot(xx,s22_miss,'color',C(4,:),'LineWidth',3);
legend('2-enh 29C','no primary 29C','2-enh 22C','no primary 22C');
set(gca,'FontSize',15); xlabel('fraction inactive nuclei');
% Stats
V{1} = nonzeros(sp29_miss_rate);
V{2} = nonzeros(s29_miss_rate);
V{3} = nonzeros(sp22_miss_rate);
V{4} = nonzeros(s22_miss_rate);
P_dot = zeros(4,4);
for i=1:4
for j=1:4
P_dot(i,j) = log10(ranksum(V{i},V{j}));
end
end
gn = {'2-enh 29C','no primary 29C','2-enh 22C','no primary 22C'};
figure(5); clf; imagesc(P_dot); colorbar; colormap('cool');
set(gca,'YtickLabel', str2mat(gn{:}),'YTick',1:4,'fontsize',15,...
'YMinorTick','on'); title('dots');
%%
load([folder,'/',s29_root,'03','_data.mat']); %'06'
%load([folder,'/',sp29_root,'23','_data.mat']);
figure(1); clf; imshow(handles.It);
% I = handles.It;
% I(:,:,3) = 1.4*I(:,:,3);
% figure(1); clf; imshow(1.5*I);
ints = sort(double(handles.Im1(:)));
mV = ints(round(.996*length(handles.Im1(:))));
Im1 = imadjust(handles.Im1,[12/255,mV/255]);
Cell_bnd = false(h,w); Cell_bnd(handles.cell_bords) = 1;
Cell_bnd = imdilate(Cell_bnd,strel('disk',1));
figure(2); clf;
Io = uint8(zeros(h,w,3));
Io(:,:,1) = mV; % Im1;
Io(:,:,2) = imadd(uint8(0*L2.*Cell_bnd),0*handles.Im2); % imadd(uint8(255*Cell_bnd),1*handles.Im2); %
Io(:,:,3) = imadd(uint8(255*Cell_bnd),0*handles.In); % uint8(255*Cell_bnd); %
% Io = uint8(bsxfun(@times,double(Io)/155,double(handles.In)));
clf; imshow(Io); hold on;
title(['embryo ',emb],'FontSize',15); pause(2);
figure(5);
Io = uint8(zeros(h,w,3));
Io(:,:,2) = imadd(uint8(0*L2.*Cell_bnd),1*handles.Im2); % imadd(uint8(255*Cell_bnd),1*handles.Im2); %
% Io = uint8(bsxfun(@times,double(Io)/155,double(handles.In)));
clf; imshow(Io); hold on;
title(['embryo ',emb],'FontSize',15); pause(2);
%%
for n=1:N
if n<10
emb = ['0',num2str(n)];
else
emb = num2str(n);
end
% emb = '02', 11,12,27; % sp22
% emb = '10'; % s22
% emb = '26'; % sp29
% emb = '06' % s29
try %
load([folder,'/',s29_root,emb,'_data.mat']);
%figure(3); clf; hist(double(handles.Im1(:)),200);
%
cell_int = H;
Nnucs = max(H(:));
mu_I = zeros(Nnucs,1);
% sig_I = zeros(Nnucs,1);
mu_N = zeros(Nnucs,1);
reg_data = regionprops(H,'PixelIdxList');
for i=1:Nnucs;
pixes = reg_data(i).PixelIdxList;
mu_I(i) = median(handles.Im1(pixes));
mu_N(i) = median(handles.In(pixes));
% sig_I(i) = std(double(handles.Im1(pixes)));
cell_int(pixes) = mu_I(i);
end
cell_int = uint8( 255*cell_int./max(cell_int(:)) );
% figure(4); clf; imshow(cell_int);
%
Cell_bnd = false(h,w);
Cell_bnd(handles.cell_bords) = 1;
Cell_bnd = imdilate(Cell_bnd,strel('disk',1));
% Im1 = flipud(fliplr(Im1));
% L1 = flipud(fliplr(L1));
% L2 = flipud(fliplr(L2));
% Cell_bnd = flipud(fliplr(Cell_bnd));
% cell_int = flipud(fliplr(cell_int));
% handles.In = flipud(fliplr(handles.In));
% handles.Im2 = flipud(fliplr(handles.Im2));
figure(3); clf;
Io = uint8(zeros(h,w,3));
Io(:,:,1) = imadd(imadd(imadd(.6*cell_int,handles.Im1), .3*handles.In),uint8(125*L2.*Cell_bnd));
Io(:,:,2) = imadd( imadd(uint8(125*L2.*Cell_bnd),0*handles.Im2), .3*handles.In); % imadd(uint8(255*Cell_bnd),1*handles.Im2); %
Io(:,:,3) = imadd(uint8(0*L2.*Cell_bnd),.3*handles.In); % uint8(255*Cell_bnd); %
% Io = uint8(bsxfun(@times,double(Io)/155,double(handles.In)));
clf; imshow(Io); hold on;
title(['embryo ',emb],'FontSize',15); pause(2);
catch
end
end
%%
load([folder,'/',sp29_root,'26','_data.mat']); % s29_12 sp29 26
figure(1); clf; imshow(handles.It);
cell_int = H;
Nnucs = max(H(:));
mu_I = zeros(Nnucs,1);
reg_data = regionprops(H,'PixelIdxList');
for i=1:Nnucs;
pixes = reg_data(i).PixelIdxList;
mu_I(i) = median(handles.Im1(pixes));
cell_int(pixes) = mu_I(i);
end
cell_int = uint8( 255*cell_int./max(cell_int(:)));
s29_DI = uint8(bsxfun(@times,double(cell_int)/255,double(handles.Im1)));
C = jet(70); C = [zeros(3,3);C;ones(300,3)];
figure(4); clf; imagesc(s29_DI); colormap(C);
s29_DI = uint8(bsxfun(@times,double(cell_int)/255,double(handles.In)));
C = jet(200); C = [zeros(3,3);C;ones(50,3)];
figure(5); clf; imagesc(s29_DI); colormap(C);
%%
x = linspace(0,1,10);
figure(1); clf;
hist(nonzeros(sp29_miss_rate),x);
hblock = findobj(gca,'type','patch');
set(hblock,'FaceColor','r','EdgeColor','k');
hold on;
hist(nonzeros(s29_miss_rate),x); alpha(.6);
xlim([min(x)-.05,max(x)]);
set(gca,'FontSize',17);
xlabel('Fraction missing reporter');
set(gcf,'Color','w');
legend('sog2enh, 29C','sogS, 29C');
x = linspace(0,1,10);
figure(2); clf;
hist(nonzeros(sp29_miss_rate),x);
hblock = findobj(gca,'type','patch');
set(hblock,'FaceColor','r','EdgeColor','k');
hold on;
hist(nonzeros(sp22_miss_rate),x); alpha(.6);
xlim([min(x)-.05,max(x)]);
set(gca,'FontSize',17);
xlabel('Fraction missing reporter');
set(gcf,'Color','w');
legend('sog2enh, 29C','sog2enh, 22C');
%%
figure(2); clf;
Io = uint8(zeros(h,w,3));
Io(:,:,1) = uint8(255*L1);
Io(:,:,2) = uint8(255*L2);
Io(:,:,3) = 30*handles.In;
DI = uint8(bsxfun(@times,double(Io)/255,double(handles.In)));
clf; imshow(DI);
for k=1:handles.Rs1
hold on; plot(bndrys1{k}(:,1),bndrys1{k}(:,2),'r','LineWidth',3);
end
for k=1:handles.Rs2
hold on; plot(bndrys2{k}(:,1),bndrys2{k}(:,2),'g','LineWidth',3);
end
hold on;
plot(rna_x1,rna_y1,'r.');
plot(rna_x2,rna_y2,'g.');
Nnucs_on1 = length(pts1)
Nnucs_on2 = length(pts2)
on1_not_2 = setdiff(pts1,pts2);
on2_not_1 = setdiff(pts2,pts1);
cnt_1not2 = length(on1_not_2);
cnt_2not1 = length(on2_not_1);